atb - Lab Notebook

Maron lab

2025/07/11 Preprocessing some human samples.
2025/06/13 Preprocessing some human samples.
2025/06/12 Preprocessing some human samples.
2025/05/21 Preprocessing some human samples.
2025/05/20 Preprocessing some human samples.
2025/05/19 Preprocessing some human samples.

Kim lab

2025/02/28 Examining various adipose ferritin transporter samples.
2024/12/06 Examining various adipose ferritin transporter samples.
2024/12/03 Kim Lab: IDD v IAD (Added GSEA)
2024/11/08 Preprocessing various adipose ferritin transporter samples.

Speer lab

2024/09/25 axonTRAP_spearC
2024/09/18 Analyses of the IPRGC re-processed samples.
2024/09/12 Analyses of the IPRGC re-processed samples.
2024/09/10 Analyses of the IPRGC re-processed samples.
2024/08/21 An initial exploration of the IPRGC re-processed samples.
2024/08/09 Analyses of the IPRGC re-processed samples.
2024/08/08 Preprocessing the IPRGC samples de-novo.
2024/08/04 An initial exploration of the IPRGC re-processed samples.
2024/05/30 Preprocessing the IPRGC samples de-novo.
2023/09/29 Sequencing the genome of 5 WT/het/KO IPRGC mice: 202309
2020/11/10 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/11/10 plotly
2020/11/10 gg
2020/11/10 gg
2020/11/09 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/10/30 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/10/26 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/10/09 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/10/08 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/16 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/15 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/14 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/10 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/09 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.
2020/01/08 M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.

Lee lab

2024/08/02 Querying a set of Pseudomonas strains, and vibrio later
2023/05/01 Querying a set of Pseudomonas strains.
2023/04/20 Querying a set of Pseudomonas strains.
2022/10/25 Searching for Pseudomonas following catheter removal.
2022/07/01 ED Project: Pseudomonas RNASeq dataset.
2022/06/30 Some Pseudomonas RNAseq data: SK.
2022/05/12 ED Project: Pseudomonas RNASeq dataset.
2022/04/05 Examining the Pseudomonas ORFeome via deep sequencing of a plasmid library.
2022/04/04 Examining the Pseudomonas ORFeome via deep sequencing of a plasmid library.
2022/03/04 ED Project: Pseudomonas RNASeq dataset.
2022/03/01 Some Pseudomonas RNAseq data: SK.
2022/02/24 Examining the Pseudomonas ORFeome via deep sequencing of a plasmid library.
2022/02/02 Some Pseudomonas RNAseq data: SK.
2022/02/02 Some Pseudomonas RNAseq data: SM.
2022/01/31 Some Pseudomonas RNAseq data: SK.
2022/01/31 Some Pseudomonas RNAseq data: SM.
2020/01/13 P. aeruginosa 20190720: Cross reference putative SNPs across samples.
2019/07/29 P. aeruginosa 20190720: Cross reference putative SNPs across samples.
2019/07/15 P. aeruginosa 20190720: Cross reference putative SNPs across samples.
2018/11/05 20170718: RNAseq of P.aeruginosa.
2018/08/27 20180718: kP. aeruginosa sample estimation.
2018/07/24 20171019: P.aeruginosa 2017: annotation data
2018/07/24 20171019: P. aeruginosa sample estimation.
2018/07/24 20171019: RNAseq of P.aeruginosa, more samples!
2018/07/24 20171019: RNAseq of P.aeruginosa.
2018/07/24 20171019: Pseudomonas aeruginosa mers: comparing 4mer old/new data.
2018/07/24 20171019: RNAseq of P.aeruginosa, Ontology searching.
2018/07/24 20171019: Pseudomonas aeruginosa mers, comparing 5mer old/new data.
2018/07/24 20171019: Pseudomonas aeruginosa mers: comparing 6mer old/new data.
2018/07/24 20171019: Pseudomonas aeruginosa mers: comparing 7mer old/new data.
2018/07/24 20171019: Pseudomonas aeruginosa mers: comparing old/new 8mer data
2018/07/24 20170620: Quick coverage estimates for Pseudomonas aeruginosa.
2018/07/24 20170720: Small RNA samples from Pseudomonas aeruginosa
2018/07/24 20170705: Preprocessing Small RNA samples from Pseudomonas aeruginosa
2018/07/24 20170425: Random Venn diagrams for VTLee.
2018/07/24 20170718 P.aeruginosa: annotation data

McIver lab

2024/06/10 Examining two streptococcal strains, two media, one supplement, and two timepoints.
2023/03/16 S. agalactiae 202303: Examining reads from input, blood, and brain.
2023/03/14 S. agalactiae 202303: Examining reads from input, blood, and brain.
2023/03/10 S. agalactiae 202210: Examining reads from input, blood, and brain.
2023/03/09 S. agalactiae 202210: Examining reads from input, blood, and brain.
2023/02/01 S.pyogenes 5448 202301: RNASeq comparing rofA strains across time.
2022/08/18 S.pyogenes 5448 rnaseq comparing pdxR strains across time.
2022/04/26 S.pyogenes 5448 rnaseq comparing pdxR strains across time.
2022/04/26 S.pyogenes 5448 rnaseq comparing rofA strains across time.
2022/04/25 S.pyogenes 5448 rnaseq comparing pdxR strains across time.
2022/04/25 S.pyogenes 5448 rnaseq comparing rofA strains across time.
2022/02/02 gg
2021/12/07 RNA/TNSeq of S.pyogenes 5448: rpoE influence on gene expression
2021/10/22 Compare prodigal runs from two parameter sets.
2021/10/14 I am not certain what to title this.
2021/06/02 S. agalactiae 202105: Poking at some TNSeq.
2021/01/28 S. agalactiae 202010: Poking at some TNSeq.
2020/10/15 S. agalactiae 20191105: Poking at some TNSeq.
2020/07/03 S. agalactiae 20191105: Poking at some TNSeq.
2020/02/11 S. agalactiae 20191105: Poking at some TNSeq.
2019/11/06 S. agalactiae 20191105: Poking at some TNSeq.
2019/09/17 S.pyogenes 5005 rnaseq: 3 genotypes, 2 media types.
2019/09/16 S.pyogenes 5005 rnaseq: 3 genotypes, 2 media types.
2018/07/17 Differential Expression for TNSeq of Spyogenes. (2017)
2018/07/17 S.pyogenes 2017: TNSeq index.
2018/07/17 Sample estimation for TNSeq of Spyogenes (2017 including Andrew).
2018/07/17 Annotation data for RNAseq/TNSeq of S.pyogenes (2017)
2018/03/30 S.pyogenes 2016: TNSeq of strain HSC5 in differing media.
2018/03/30 S.pyogenes 2016: RNASeq analyses pre-hpgltools
2018/03/30 S.pyogenes 2016: scatter plot of gene abundances.
2018/03/30 S.pyogenes 2015: Initial analyses index.
2018/03/30 S.pyogenes 2015: Using the original analyses.
2018/03/30 S.pyogenes 2015 TNSeq: First visualizations of tnseq data.
2018/03/28 S.pyogenes 201505: 0 mismatch analyses.
2018/03/27 2015: The first TNSeq of S.pyogenes
2017/10/06 S.pyogenes TNSeq questions
2017/06/09 Annotation data for RNAseq/TNSeq of S.pyogenes
2017/06/09 RNA/TNSeq of S.pyogenes 5448: Subcutaneous infection
2016/09/14 RNA/TNSeq of S.pyogenes 5448: cpsY influence on gene expression
2016/09/14 RNAseq/TNSeq of S.pyogenes strain 5448.
2016/08/10 RNA/TNSeq of S.pyogenes 5448: RNA Expression over time in THY.
2016/08/08 RNA/TNSeq of S.pyogenes 5448: TNSeq Fitness over time in THY.
2016/08/06 Preprocessing RNAseq/TNSeq samples from Streptococcus pyogenes strain 5448.
2016/07/29 Sample metrics: RNAseq/TNSeq of S.pyogenes
2016/07/29 Sample metrics: RNAseq/TNSeq of S.pyogenes
2016/06/06 TNSeq of S.pyogenes strain HSC5 in differing media.

TMRC

2024/04/16 TMRC2 202401: Promastigote (mostly) Differential Expression Analyses.
2024/04/16 TMRC2 202401: Visualizing Analyses before DE/variant analyses
2024/04/16 TMRC2 202401: Data Set Creation
2024/04/16 TMRC2 202404: Macrophage Differential Expression.
2024/04/16 TMRC2 Macrophages 202404: Data Set Creation
2024/04/16 TMRC2 202404: Visualizing Macrophage samples.
2023/11/07 An analysis of cutaneous leishmaniasis biopsies: Sys.getenv('VERSION')
2023/11/07 TMRC3 202308: Creating Data Structures
2023/08/03 sankeyNetwork
2023/05/12 sankeyNetwork
2023/05/10 sankeyNetwork
2021/06/15 L. panamensis 202106: A Macrophage Side Experiment
2021/05/30 L. panamensis 202105: A Separate Macrophage Experiment
2021/05/30 L. panamensis 202105: A Separate Macrophage Experiment
2021/05/07 Quick and dirty comparison of hisat2 vs Dragen’s salmon
2021/05/06 Some macrogen samples
2021/05/05 Some macrogen samples
2021/05/05 Some macrogen samples
2020/11/08 L. panamensis 202011: A Macrophage Side Experiment
2020/11/08 L. panamensis 202011: A Macrophage Side Experiment
2020/11/06 L. panamensis 202011: A Macrophage Side Experiment
2020/01/08 L. panamensis 20200103: Sample Estimation.
2020/01/08 L. panamensis 20200103: Sample Estimation.
2020/01/03 L. panamensis 20200103: Sample Estimation.
2019/10/04 L. panamensis 20191001: Sample Estimation
2019/10/04 L. panamensis 20191001: Sample Estimation
2019/10/03 L. panamensis 20191001: Collecting annotation information.
2019/10/03 L. panamensis 20191001: Collecting annotation information.
2019/10/01 L. panamensis 20191001: Collecting annotation information.
2019/10/01 L. panamensis 20191001: Collecting annotation information.

Splicing

2024/04/05 Exploring splicing in our infected/uninfected macrophage samples.

Hill lab

2024/02/15 Examining an experiment in mouse embryogenesis.
2024/02/06 Examining an experiment in mouse embryogenesis.
2024/02/05 Examining an experiment in mouse embryogenesis.
2024/02/01 Examining an experiment in mouse embryogenesis.
2024/01/31 Preprocessing some new samples!

Briken lab

2024/01/08 Sequencing 3 Mycobacterium Tuberculosis strains.
2024/01/03 Sequencing 3 Mycobacterium Tuberculosis strains.
2023/12/07 Sequencing 3 Mycobacterium Tuberculosis strains.
2023/12/06 Sequencing 3 Mycobacterium Tuberculosis strains.
2023/06/01 Splitting a large dataset, running cellpose, and measuring the results using fiji tracker.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Splitting a large dataset, running cellpose, and measuring the results.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/06/01 Notes for Jacques images.
2023/04/03 Notes for Jacques images.
2020/07/21 2020 Mtb. analyses.
2020/06/17 Scatter plot of delta/complement DIA SWATH
2020/06/17 Scatter plot of whole complement/delta DIA SWATH
2020/06/17 Scatter plot of delta/wt culture filtrate DIA SWATH
2020/06/17 Scatter plot of culture filtrate delta/wt DIA SWATH
2020/06/17 Scatter plot of whole cell delta/wt DIA SWATH
2020/06/15 20200320 Mtb. analyses.
2020/06/12 20200320 Mtb. analyses.
2020/01/13 plotly
2019/12/10 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/12/09 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/11/15 plotly
2019/10/29 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/10/22 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/21 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/18 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/18 M.tuberculosis 20190801 proteomics: Collecting annotation data.
2019/10/17 M.tuberculosis 20190718 proteomics: Collecting annotation data.
2019/10/17 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2019/08/22 M.tuberculosis 20190718: Most samples! Analyzing data OpenSwathWorkFlow/TRIC.
2019/08/19 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2019/08/19 M.tuberculosis 20190718 proteomics: Preprocessing.
2019/07/31 M.tuberculosis 20190718 proteomics: Preprocessing.
2019/07/01 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/26 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/26 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/24 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/20 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/20 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/07 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/07 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/05/22 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/03 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/02 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/01 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/04/30 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/15 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/12 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/11 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/03/14 Compare different DIA quantification methods.
2018/11/19 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/11/12 M.tuberculosis 20181112 proteomics: Collecting annotation data.
2018/11/07 M.tuberculosis 20180913: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/10/31 M.tuberculosis 20180913 proteomics: Collecting annotation data.
2018/10/26 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2018/09/11 M.tuberculosis 20180817: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/09/06 M.tuberculosis 20180817 proteomics: Collecting annotation data.
2018/08/16 M.tuberculosis 20180806: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/08/06 M.tuberculosis 20180729: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/07/31 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC (20180720).
2018/06/14 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/06/14 M.tuberculosis 20180611 proteomics: Collecting annotation data.
2018/06/11 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/30 M.tuberculosis 20180530: Preprocessing DIA data with a comet highres library (more samples).
2018/05/30 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/17 M.tuberculosis 201805: Preprocessing DIA data with a comet highres library (more samples).
2018/05/17 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/04/27 M.tuberculosis 2018: Compare kallisto and salmon
2018/04/25 M.tuberculosis 2018: Alternative splicing, suppa.
2018/04/20 M.tuberculosis 2018 proteomics: Introduction/TODO list.
2018/04/20 M.tuberculosis 2017 proteomics: Annotation data for proteomics analyses (uniprot).
2018/04/20 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/20 M.tuberculosis 2018: Comparing CID and HCD libraries.
2018/04/19 M.tuberculosis 2016: A small collection of analyses.
2018/04/19 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/18 M.tuberculosis 2018: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/04/18 M.tuberculosis 2018 proteomics: Collecting annotation data.
2018/04/18 M.tuberculosis 2018: Preprocessing DIA data with a comet highres library.
2018/04/09 M.tuberculosis 201711: Evaluating some MS/MS peptide search metrics.
2018/04/04 M.tuberculosis 2017: Collecting annotation data.
2018/03/30 M.tuberculosis 2017: Testing out Proteomics analyses.
2018/03/30 M.tuberculosis 2017: Relative PE protein expression.
2018/03/29 M.tuberculosis splicing 2018: Annotation data.

Lpanamensis Host transcriptome

2023/09/19 TMRC3 202308: Creating Data Structures
2023/09/01 TMRC3 202308: Visualizing Analyses
2023/08/31 TMRC3 202308: Visualizing Analyses
2023/08/30 TMRC3 202308: Visualizing Analyses
2023/08/30 TMRC3 202308: Creating Data Structures
2023/08/09 TMRC3 202305: Differential Expression analyses
2023/08/01 TMRC3 ML Classification of outcome: 202305
2023/07/28 TMRC3 202305: Creating Data Structures
2023/07/26 TMRC3 ML Classification of outcome: 202305
2023/07/19 TMRC3 202305: Creating Data Structures
2023/07/11 TMRC3 202305: Differential Expression analyses, Tumaco only
2023/07/10 TMRC3 202305: Differential Expression analyses, Tumaco only
2023/07/10 TMRC3 202305: Differential Expression analyses, both clinics.
2023/07/10 TMRC3 202305: Creating Data Structures
2023/07/09 TMRC3 202305: Creating Data Structures
2023/07/09 TMRC3 202305: Differential Expression analyses
2023/07/08 TMRC3 202305: Differential Expression analyses
2023/07/07 TMRC3 202305: Differential Expression analyses
2023/07/06 TMRC3 202305: Differential Expression analyses
2023/07/06 TMRC3 ML Classification of outcome: 202302
2023/07/05 TMRC3 202305: Differential Expression analyses
2023/06/12 TMRC3 202305: Differential Expression analyses
2023/05/25 TMRC3 202304: Differential Expression analyses
2023/05/25 TMRC3 202305: Visualizing Analyses
2023/05/25 TMRC3 202305: Visualizing Analyses
2023/05/24 TMRC3 202305: Creating Data Structures
2023/05/18 TMRC3 202304: Creating Data Structures
2023/05/17 TMRC3 202304: Creating Data Structures
2023/05/15 TMRC3 202304: Visualizing Analyses
2023/05/11 TMRC3 202304: Creating Data Structures
2023/05/08 TMRC3 202304: Creating Data Structures
2023/04/27 TMRC3 202304: Differential Expression analyses
2023/04/26 TMRC3 202304: Visualizing Analyses
2023/04/26 TMRC3 202304: Creating Data Structures
2023/03/17 TMRC3 202301: Creating Data Structures
2023/03/07 TMRC3 202301: Visualizing Analyses
2023/03/01 TMRC3 202301: Creating Data Structures
2023/02/28 TMRC3 202301: Differential Expression analyses
2023/02/27 TMRC3 202301: Visualizing Analyses
2023/02/27 TMRC3 202301: Differential Expression analyses
2023/02/26 TMRC3 202301: Visualizing Analyses
2023/02/25 TMRC3 202301: Creating Data Structures
2023/02/24 TMRC3 202301: Visualizing Analyses
2023/02/24 TMRC3 202301: Creating Data Structures
2023/02/22 TMRC3 202301: Creating Data Structures
2023/02/14 TMRC3 202301: Creating Data Structures
2023/01/27 L. panamensis 202212: TMRC3 Differential Expression analyses
2023/01/25 L. panamensis 202212: TMRC3 Differential Expression analyses
2023/01/11 TMRC3 202212: Creating Data Structures
2023/01/06 L. panamensis 202212: Creating TMRC3 Data Structures
2023/01/04 L. panamensis 202212: Creating TMRC3 Data Structures
2023/01/03 L. panamensis 202212: TMRC3 Differential Expression analyses
2022/12/29 L. panamensis 202212: Visualizing TMRC3 Analyses
2022/12/29 L. panamensis 202212: Creating TMRC3 Data Structures
2022/12/13 L. panamensis 202212: TMRC3 Differential Expression analyses
2022/12/12 L. panamensis 202212: Visualizing TMRC3 Analyses
2022/12/12 L. panamensis 202212: Creating TMRC3 Data Structures
2022/12/09 L. panamensis 202212: Visualizing TMRC3 Analyses
2022/12/09 L. panamensis 202212: Creating TMRC3 Data Structures
2022/12/09 L. panamensis 202212: TMRC3 Differential Expression analyses
2022/12/08 L. panamensis 202212: Visualizing TMRC3 Analyses
2022/12/08 L. panamensis 202212: Creating TMRC3 Data Structures
2022/12/05 L. panamensis 202209: Creating TMRC3 Data Structures
2022/11/29 L. panamensis 202209: Differential Expression analyses
2022/10/28 L. panamensis 202209: Differential Expression analyses
2022/10/27 L. panamensis 202209: Creating TMRC3 Data Structures
2022/10/21 L. panamensis 202209: Creating TMRC3 Data Structures
2022/10/19 L. panamensis 202209: Differential Expression analyses
2022/10/15 L. panamensis 202209: Differential Expression analyses
2022/10/13 L. panamensis 202209: Likelihood Ratio Tests and GSVA
2022/10/12 L. panamensis 202209: Creating TMRC3 Data Structures
2022/09/21 L. panamensis 202207: Create TMRC3 Data Structures
2022/08/17 L. panamensis 202207: Likelihood Ratio Tests and GSVA
2022/08/17 L. panamensis 202207: Create TMRC3 Data Structures
2022/08/04 L. panamensis 202207: Create TMRC3 Data Structures
2022/08/03 L. panamensis 202207: Differential Expression analyses
2022/08/02 L. panamensis 202207: Differential Expression analyses
2022/08/01 L. panamensis 202207: Differential Expression analyses
2022/08/01 L. panamensis 202207: Visualizing TMRC3 Analyses
2022/07/29 L. panamensis 202207: Visualizing TMRC3 Analyses
2022/07/28 L. panamensis 202207: Create TMRC3 Data Structures
2022/07/27 L. panamensis 202207: Differential Expression analyses
2022/07/15 L. panamensis 202207: Visualizing TMRC3 Analyses
2022/07/15 L. panamensis 202207: Create TMRC3 Data Structures
2022/07/14 L. panamensis 202207: Create TMRC3 Data Structures
2022/07/12 L. panamensis 202206: Visualizing TMRC3 Analyses
2022/07/11 L. panamensis 202206: Visualizing TMRC3 Analyses
2022/07/08 L. panamensis 202206: Create Data Structures
2022/07/08 L. panamensis 202206: Visualizing TMRC3 Analyses
2022/07/07 L. panamensis 202206: Create Data Structures
2022/06/23 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/06/08 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/06/03 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/06/02 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/05/19 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/05/06 L. panamensis 202205: Reorganizing TMRC3 Analyses
2022/04/29 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/04/28 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/04/07 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/04/05 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/04/04 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/04/01 L. panamensis 202203: Reorganizing TMRC3 Analyses
2022/03/09 L. panamensis 202202: Reorganizing TMRC3 Analyses
2022/03/02 L. panamensis 202202: Reorganizing TMRC3 Analyses
2022/02/16 L. panamensis 202011: Reorganizing TMRC3 Analyses
2022/02/04 L. panamensis 202011: Reorganizing TMRC3 Analyses
2022/01/21 L. panamensis 202011: Reorganizing TMRC3 Analyses
2022/01/13 L. panamensis 202011: Reorganizing TMRC3 Analyses
2022/01/04 L. panamensis 202011: Reorganizing TMRC3 Analyses
2022/01/03 L. panamensis 202011: Reorganizing TMRC3 Analyses
2021/12/31 L. panamensis 202011: Reorganizing TMRC3 Analyses
2021/11/19 TMRC3 Comprehensive Data Analysis: 202111
2021/11/11 TMRC3 Comprehensive Data Analysis: 202111
2021/11/03 TMRC3 Comprehensive Data Analysis: 202110
2021/11/02 TMRC3 Comprehensive Data Analysis: 202110
2021/10/29 TMRC3 Comprehensive Data Analysis: 202110
2021/10/13 TMRC3 Comprehensive Data Analysis: 202110
2021/06/29 TMRC3 Comprehensive Data Analysis: 202106
2021/06/14 TMRC3 Comprehensive Data Analysis: 202106
2021/06/14 TMRC3 Comprehensive Data Analysis: 202106
2021/06/11 TMRC3 Comprehensive Data Analysis: 202106
2021/06/11 TMRC3 Comprehensive Data Analysis: 202106
2021/06/08 TMRC3 Comprehensive Data Analysis: 202106
2021/06/02 TMRC3 Comprehensive Data Analysis: 202105
2021/06/02 TMRC3 Comprehensive Data Analysis: 202105
2021/05/31 TMRC3 Comprehensive Data Analysis: 202105
2021/05/30 TMRC3 Comprehensive Data Analysis: 202105
2021/05/29 TMRC3 Comprehensive Data Analysis: 202105
2021/05/29 TMRC3 Comprehensive Data Analysis: 202105
2021/05/28 TMRC3 Comprehensive Data Analysis: 202105
2021/05/28 TMRC3 Comprehensive Data Analysis: 202105
2021/05/27 TMRC3 Comprehensive Data Analysis: 202105
2021/05/17 TMRC3 Comprehensive Data Analysis: 202104
2021/05/16 TMRC3 Comprehensive Data Analysis: 202104
2021/05/16 TMRC3 Comprehensive Data Analysis: 202104
2021/05/14 TMRC3 Comprehensive Data Analysis: 202104
2021/05/14 TMRC3 Comprehensive Data Analysis: 202104
2021/05/13 TMRC3 Comprehensive Data Analysis: 202104
2021/05/13 TMRC3 Comprehensive Data Analysis: 202104
2021/04/23 TMRC3 Comprehensive Data Analysis: 202104
2021/04/22 TMRC3 Comprehensive Data Analysis: 202103
2021/04/22 TMRC3 Comprehensive Data Analysis: 202103
2021/04/20 TMRC3 Comprehensive Data Analysis: 202103
2021/04/20 TMRC3 Comprehensive Data Analysis: 202103
2021/04/16 TMRC3 Comprehensive Data Analysis: 202103
2021/04/16 TMRC3 Comprehensive Data Analysis: 202103
2021/04/07 TMRC3 Comprehensive Data Analysis: 202103
2021/04/07 TMRC3 Comprehensive Data Analysis: 202103
2021/04/06 TMRC3 Comprehensive Data Analysis: 202103
2021/04/06 TMRC3 Comprehensive Data Analysis: 202103
2021/04/05 TMRC3 Data Analysis: 202103
2021/04/05 TMRC3 Data Analysis: 202103
2021/03/31 L. panamensis 202103: TMRC3 Sample Estimation
2021/03/29 L. panamensis 202103: TMRC3 Sample Estimation
2021/03/29 L. panamensis 202103: TMRC3 Sample Estimation
2021/01/18 L. panamensis 202011: TMRC3 Sample Estimation
2021/01/06 L. panamensis 202011: TMRC3 Sample Estimation
2021/01/06 L. panamensis 202011: TMRC3 Sample Estimation
2020/11/18 L. panamensis 202011: TMRC3 Sample Estimation
2020/11/11 L. panamensis 202011: TMRC3 Sample Estimation
2020/10/29 L. panamensis 202009: TMRC3 Sample Estimation
2020/10/14 L. panamensis 202009: TMRC3 Sample Estimation
2020/10/14 L. panamensis 202009: TMRC3 Sample Estimation
2020/09/30 L. panamensis 202009: TMRC3 Sample Estimation
2020/09/28 L. panamensis 202009: Sample Estimation
2020/09/28 L. panamensis 202009: Sample Estimation
2020/09/22 L. panamensis 202009: Sample Estimation
2020/09/22 L. panamensis 202009: Sample Estimation
2019/12/12 L. panamensis 20191001: Sample Estimation
2019/12/12 L. panamensis 20191001: Sample Estimation
2019/12/11 L. panamensis 20191001: Sample Estimation
2019/12/11 L. panamensis 20191001: Sample Estimation

Oncomelania

2023/09/08 Comparing Oncomelania transcriptomes pre/post infection.
2023/08/03 Comparing Oncomelania transcriptomes pre/post infection.

Lpanamensis Parasite transcriptome

2023/07/19 TMRC2 202305: Promastigote (mostly) Differential Expression Analyses.
2023/07/19 TMRC2 202305: Data Set Creation
2023/07/06 TMRC2 202305: Data Set Creation
2023/07/06 TMRC2 202305: Promastigote (mostly) Differential Expression Analyses.
2023/07/05 TMRC2 202305: Promastigote (mostly) Differential Expression Analyses.
2023/07/05 TMRC2 202305: Visualizing Analyses following differential expression
2023/07/03 TMRC2 202305: Visualizing Analyses following differential expression
2023/07/03 TMRC2 202305: Visualizing Analyses before DE/variant analyses
2023/07/03 TMRC2 202305: Promastigote (mostly) Differential Expression Analyses.
2023/06/30 TMRC2 202305: Data Set Creation
2023/06/29 TMRC2 202305: Data Set Creation
2023/05/30 TMRC2 202305: Data Set Creation
2023/05/25 TMRC2 202305: Data Set Creation
2023/05/25 TMRC2 202304: Data Set Creation
2023/05/24 TMRC2 202305: Data Set Creation
2023/05/10 TMRC2 202304: Data Set Creation
2023/05/02 TMRC2 202304: Macrophage Differential Expression.
2023/05/02 TMRC2 202301: Visualizing Macrophage samples.
2023/05/01 TMRC2 202304: Data Set Creation
2023/04/14 TMRC2 202304: Data Set Creation
2023/04/13 TMRC2 202304: Data Set Creation
2023/04/12 TMRC2 202301: Macrophage Differential Expression.
2023/04/12 TMRC2 202302: Data Set Creation
2023/04/05 TMRC2 202301: Macrophage Differential Expression.
2023/03/09 TMRC2 202302: Data Set Creation
2023/03/08 TMRC2 202302: Data Set Creation
2023/03/03 TMRC2 202301: Macrophage Differential Expression.
2023/03/01 TMRC2 202301: Macrophage Differential Expression.
2023/02/24 TMRC2 202302: Data Set Creation
2023/02/03 TMRC2 ML Classification of strains using variants: 202301
2023/01/31 TMRC2 202301: Data Set Creation
2023/01/26 TMRC2 202301: Data Set Creation
2023/01/26 TMRC2 202301: Visualizing Analyses before DE/variant analyses
2023/01/26 TMRC2 202301: Promastigote (mostly) Differential Expression Analyses.
2023/01/26 TMRC2 202301: Visualizing Analyses following differential expression
2023/01/25 TMRC2 202301: Visualizing Analyses following differential expression
2023/01/25 TMRC2 202301: Macrophage Differential Expression.
2023/01/25 TMRC2 202301: Data Set Creation
2023/01/24 TMRC2 202301: Promastigote (mostly) Differential Expression Analyses.
2023/01/24 TMRC2 202301: Macrophage Differential Expression.
2023/01/23 TMRC2 202301: Macrophage Differential Expression.
2023/01/20 TMRC2 Data Set Creation: 202301
2023/01/19 TMRC2 202301: Visualizing Macrophage samples.
2023/01/18 TMRC2 Data Set Creation: 202301
2023/01/18 TMRC2 202212: Macrophage Differential Expression.
2023/01/17 TMRC2 Data Set Creation: 202301
2023/01/17 TMRC2 ML Classification of strains: 202212
2023/01/05 TMRC2 202212: Visualizing Macrophage samples.
2023/01/04 TMRC2 Data Set Creation: 202212
2022/12/08 TMRC2 Data Set Creation: 202212
2022/12/05 L. panamensis 202209: TMRC2 Differential Expression Analyses
2022/10/03 L. panamensis 202209: TMRC2 Macrophage Differential Expression.
2022/09/28 L. panamensis 202209: TMRC2 Macrophage Differential Expression.
2022/09/27 L. panamensis 202209: TMRC2 Macrophage Differential Expression.
2022/09/26 L. panamensis 202209: TMRC2 Macrophage Differential Expression.
2022/09/19 L. panamensis 202209: Visualizing TMRC2 Analyses before DE/variant analyses
2022/09/19 L. panamensis 202209: Visualizing TMRC2 Macrophage samples.
2022/09/16 L. panamensis 202207: Visualizing TMRC2 Analyses before DE/variant analyses
2022/09/15 L. panamensis 202209: Visualizing TMRC2 Macrophage samples.
2022/09/15 TMRC2 Data Set Creation: 202209
2022/09/13 L. panamensis 202209: TMRC2 Macrophage Differential Expression.
2022/09/13 TMRC2 Data Set Creation: 202209
2022/09/07 TMRC2 Data Set Creation: 202207
2022/08/19 L. panamensis 202207: Visualizing TMRC2 Analyses
2022/08/19 TMRC2 Data Set Creation: 202207
2022/08/16 TMRC2 Data Set Creation: 202207
2022/08/15 L. panamensis 202207: Visualizing TMRC2 Analyses
2022/08/11 TMRC2 Data Set Creation: 202207
2022/08/10 TMRC2 Data Set Creation: 202207
2022/08/08 TMRC2 Data Set Creation: 202207
2022/08/04 TMRC2 Comprehensive Data Analysis: 202204
2022/08/03 TMRC2 Comprehensive Data Analysis: 202204
2022/08/02 TMRC2 Comprehensive Data Analysis: 202204
2022/07/05 TMRC2 Comprehensive Data Analysis: 202204
2022/07/01 TMRC2 Comprehensive Data Analysis: 202204
2022/06/30 TMRC2 Comprehensive Data Analysis: 202204
2022/06/09 TMRC2 Comprehensive Data Analysis: 202204
2022/06/08 TMRC2 Comprehensive Data Analysis: 202204
2022/04/07 TMRC2 Comprehensive Data Analysis: 202201
2022/04/07 TMRC2 Infecting macrophages: 202203
2022/04/06 TMRC2 Comprehensive Data Analysis: 202201
2022/04/05 TMRC2 Comprehensive Data Analysis: 202201
2022/04/04 TMRC2 Comprehensive Data Analysis: 202201
2022/04/01 TMRC2 Comprehensive Data Analysis: 202201
2022/03/29 TMRC2 Infecting macrophages: 202203
2022/03/22 TMRC2 Infecting macrophages: 202203
2022/03/13 TMRC2 Analyses
2022/01/12 TMRC2 Comprehensive Data Analysis: 202201
2022/01/07 TMRC2 Comprehensive Data Analysis: 202201
2022/01/06 TMRC2 Comprehensive Data Analysis: 202201
2021/11/03 TMRC2 Comprehensive Data Analysis: 202108
2021/10/29 TMRC2 Comprehensive Data Analysis: 202108
2021/08/23 TMRC2 Comprehensive Data Analysis: 202108
2021/07/07 TMRC2 Comprehensive Data Analysis: 202106
2021/07/07 TMRC2 Comprehensive Data Analysis: 202106
2021/06/29 TMRC2 Comprehensive Data Analysis: 202106
2021/06/29 TMRC2 Comprehensive Data Analysis: 202106
2021/06/14 TMRC2 Comprehensive Data Analysis: 202106
2021/06/11 TMRC2 Comprehensive Data Analysis: 202106
2021/06/11 TMRC2 Comprehensive Data Analysis: 202106
2021/06/08 TMRC2 Comprehensive Data Analysis: 202106
2021/06/08 TMRC2 Comprehensive Data Analysis: 202106
2021/06/03 TMRC2 Comprehensive Data Analysis: 202106
2021/06/02 TMRC2 Comprehensive Data Analysis: 202106
2021/06/01 TMRC2 Comprehensive Data Analysis: 202106
2021/06/01 TMRC2 Comprehensive Data Analysis: 202106
2021/05/30 TMRC2 Comprehensive Data Analysis: 202105
2021/05/30 TMRC2 Comprehensive Data Analysis: 202105
2021/05/29 TMRC2 Comprehensive Data Analysis: 202105
2021/05/29 TMRC2 Comprehensive Data Analysis: 202105
2021/05/17 TMRC2 Comprehensive Data Analysis: 202105
2021/05/14 TMRC2 Comprehensive Data Analysis: 202105
2021/05/14 TMRC2 Comprehensive Data Analysis: 202105
2021/05/13 TMRC2 Comprehensive Data Analysis: 202104
2021/05/13 TMRC2 Comprehensive Data Analysis: 202104
2021/04/16 TMRC2 Comprehensive Data Analysis: 202104
2021/04/16 TMRC2 Comprehensive Data Analysis: 202104
2021/04/14 TMRC2 Comprehensive Data Analysis: 202104
2021/04/14 TMRC2 Comprehensive Data Analysis: 202104
2021/04/07 TMRC2 Comprehensive Data Analysis: 202103
2021/04/07 TMRC2 Comprehensive Data Analysis: 202103
2021/04/05 TMRC2 Comprehensive Data Analysis: 202103
2021/04/05 TMRC2 Comprehensive Data Analysis: 202103
2020/12/11 L. panamensis 20201022: Sample Estimation
2020/10/21 L. panamensis 202009: Sample Estimation
2020/09/28 L. panamensis 202009: Sample Estimation
2020/09/28 L. panamensis 202009: Sample Estimation
2020/09/25 L. panamensis 202009: Sample Estimation
2020/09/25 L. panamensis 202009: Sample Estimation
2020/09/24 L. panamensis 202009: Sample Estimation
2020/09/23 L. panamensis 202009: Sample Estimation
2020/09/23 L. panamensis 202009: Sample Estimation

Wellcome Trust

2023/07/10 Wellcome to Lina’s RNASeq analyses: 202306
2023/07/10 sankeyNetwork
2023/07/06 Wellcome to Lina’s RNASeq analyses: 202306
2023/07/03 Wellcome to Lina’s RNASeq analyses: 202306
2023/06/27 Wellcome to Lina’s RNASeq analyses: 202306
2023/06/26 Wellcome to Lina’s RNASeq analyses: 202209
2023/06/09 Wellcome to Lina’s RNASeq analyses: 202209
2023/06/07 sankeyNetwork
2022/10/19 Wellcome Kinetics: 202209
2022/09/19 Wellcome to Lina’s RNASeq analyses: 202209
2022/09/14 Wellcome to Lina’s RNASeq analyses: 202209
2022/08/19 Wellcome to Lina’s RNASeq analyses!
2022/08/15 Wellcome to Lina’s RNASeq analyses!
2021/10/06 compare two sets of biopsies.

Other

2023/05/25 Notes about TNSeq to look at prophage sequences.
2015/08/26 index.html
2015/08/26 data_input.html
2015/08/26 data_normalization.html
2015/08/26 goseq.html
2015/08/26 differential_expression.html
2015/08/26 configuration.html
2015/08/26 initial_metrics.html

Baliban lab

2023/03/31 Mmusculus with and without a Senteriditis vaccine.
2022/07/25 Mmusculus with and without a Senteriditis vaccine.
2022/07/05 Mmusculus with and without a Senteriditis vaccine.
2022/04/13 Mmusculus with and without a Senteriditis vaccine.
2022/02/28 Mmusculus with and without a Senteriditis vaccine.

Park lab

2023/03/28 Playing with some new scRNASeq data: A+B+C 202301.
2023/03/24 Playing with some new scRNASeq data: A+B+C 202301.
2023/03/16 Playing with some new scRNASeq data: A+B+C 202301.
2023/02/13 Playing with some new scRNASeq data: A+B+C 202301.
2023/02/12 Playing with some new scRNASeq data: A+B+C 202301.
2023/02/08 cellranger_control_ABC_summary.html
2023/02/05 Playing with some new scRNASeq data: A+B 202301.
2023/02/03 Playing with some new scRNASeq data: A+B 202301.
2023/01/29 Playing with some new scRNASeq data: A+B 202301.
2023/01/28 Playing with some new scRNASeq data: A+B 202301.
2023/01/27 Playing with some new scRNASeq data: A+B 202301.
2023/01/26 Playing with some new scRNASeq data: 202301.
2023/01/24 Playing with some new scRNASeq data: 202301.
2023/01/20 cellranger_mock_summary.html
2023/01/20 cellranger_in_summary.html
2023/01/20 cellranger_im_summary.html
2023/01/20 cellranger_control_summary.html
2023/01/19 Playing with some new scRNASeq data: 202301.

Misc

2023/03/17 Notes on the computers in the lab.

Li lab

2023/03/10 Histone Deacetylase 5 under/over expression in R.norvegicus.
2022/08/12 Histone Deacetylase 5 under/over expression in R.norvegicus.
2022/08/11 Histone Deacetylase 5 under/over expression in R.nornegicus.

Cao lab

2022/08/09 Lamin A vs. progerin expression in HEK 293T cells.

Mosser lab

2022/01/24 202110 Revisiting some queries about stimulation responses at 4/8/12 hours
2020/04/17 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/04/17 Experimenting with some scRNASeq data.
2020/04/15 Experimenting with some scRNASeq data.
2020/04/13 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/04/10 Human Macrophages: atb version of M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/04/08 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/04/03 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/04/02 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2
2020/03/26 Human Macrophages: M-CSF v GM-CSF: LPS, LPS+Adenosine, LPS+PGE2

Meta

2022/01/24 gg
2021/11/04 gg
2021/08/20 Lm. vs. LPS
2021/08/20 compare_lm_la_scatter.html
2021/04/27 Downloaded data sets, sample estimation.
2021/03/04 20190124 Recapitulating previous results: which genes are DE in human macrophages at 4hrs upon infection with L. major?
2021/02/22 20190417 An attempt to answer one of the big questions from Najib.
2021/01/28 Use this sheet to extract subsets of the data.
2021/01/27 Use this sheet to extract subsets of the data.
2021/01/25 20190124 parasite cell comparisons.
2020/03/05 Use this sheet to extract subsets of the data.
2020/02/28 Use this sheet to extract subsets of the data.
2020/02/27 Use this sheet to extract subsets of the data.
2020/02/25 Leishmania strain visualizations: 2020-02-25
2020/02/13 20190326 An attempt to answer one of the big questions from Najib.
2019/11/15 20190417 An attempt to answer one of the big questions from Najib.
2019/07/10 Downloaded data sets, sample estimation.
2019/07/08 Downloaded data sets, annotation collection.
2019/07/03 Downloaded data sets, sample estimation.
2019/07/03 Downloaded data sets, annotation collection.
2019/06/20 Downloaded data sets, annotation collection.
2019/04/26 20190417 An attempt to answer one of the big questions from Najib.
2019/04/22 20190417 An attempt to answer one of the big questions from Najib.
2019/04/19 20190417 An attempt to answer one of the big questions from Najib.

Adelaida lab

2021/10/06 compare two sets of biopsies.
2021/03/09 L.panamensis 202102: Differential Expression in human PBMCs followed by macrophages
2021/01/15 L.panamensis 202007: Differential Expression in human macrophages.
2021/01/15 L.panamensis 202007: Differential Expression in human PBMCs.
2021/01/14 L.panamensis 202007: Differential Expression in human PBMCs.
2021/01/13 L.panamensis 202007: Differential Expression in human macrophages.
2021/01/13 L.panamensis 202007: Differential Expression in human PBMCs.
2021/01/13 L.panamensis 20190205: Differential Expression in human macrophages.
2021/01/13 L. panamensis 20190205: Sample Estiation of Infected PBMCs.
2020/07/22 L.panamensis 202007: Differential Expression in human macrophages.
2020/07/15 L.panamensis 202007: Differential Expression in human macrophages.
2020/07/10 L.panamensis 202007: Differential Expression in human macrophages.
2020/07/09 L.panamensis 202007: Differential Expression in human macrophages.
2020/07/06 L.panamensis 2016: Annotation data.
2020/02/21 L. panamensis 20190205: Sample Estiation of Infected PBMCs.
2020/02/21 L. panamensis 20180822: Annotation data.
2019/11/07 L.panamensis 201909: Antimonial Response Sample Estimation.
2019/10/30 L.panamensis 201909: Antimonial Response Sample Estimation.
2019/10/30 L. panamensis 20190914: Annotation data.
2019/10/28 L.panamensis 201909: Antimonial Response Sample Estimation.
2019/09/16 L. panamensis 20190914: Annotation data.
2019/02/08 L. panamensis 20190205: Differential Expression of infected PBMCs.
2019/02/08 L. panamensis 20190205: Sample Estiation of Infected PBMCs.
2019/02/07 L.panamensis 2016: Differential Expression in human macrophages.
2019/02/07 L.panamensis 20180822: Sample estimation of Human macrophages.
2019/02/07 L. panamensis 20180822: Annotation data.
2019/02/06 L.panamensis 2016: Differential Expression in human macrophages.
2019/02/06 L.panamensis 20180822: Sample estimation of Human macrophages.
2019/02/06 L. panamensis 20180822: Annotation data.
2019/02/06 L.panamensis 2016: Differential Expression in human macrophages.
2019/02/06 L.panamensis 20180822: Sample estimation of Human macrophages.
2019/01/10 RNAseq of L.panamensis: Testing out GSVA
2019/01/08 L. panamensis 20190107: Differential Expression of infected PBMCs.
2019/01/04 L. panamensis 20180822: Differential Expression of infected PBMCs.
2019/01/02 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/28 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/27 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/13 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/12 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/11 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/07 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/06 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/12/05 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/11/28 L.panamensis 2016: Differential Expression in human macrophages.
2018/11/27 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/11/26 L. panamensis 20180822: Differential Expression of infected PBMCs.
2018/11/15 L. panamensis 20180822: Sample Estiation of Infected PBMCs.
2018/11/14 L. panamensis 20181114: Annotation data.
2018/11/13 L.panamensis 20180822: Variant positions.
2018/11/02 L. panamensis 20180822: Sample Estiation of Infected PBMCs.
2018/10/30 L. panamensis 20180822: Annotation data.
2018/10/16 L.panamensis 20180822: Variant positions.
2018/08/21 L.panamensis 2016: Differential Expression in human macrophages, during infection, in biopsies, and with antimonial treatment.
2018/05/02 L.panamensis 2016: Sample estimation of Human macrophages.
2018/05/01 L.panamensis 2016: Human Macrophage Differential Expression of parasite samples.
2018/05/01 L.panamensis 2016: Human macrophages during infection, in biopsies, and with antimonial treatment.
2018/04/20 L.panamensis 2016: Preprocessing RNAseq samples.
2018/04/03 RNAseq of L.panamensis: Biopsy Differential Expression.
2018/04/02 L.panamensis biopsies 2016: Sample Estimation.
2018/03/30 L.panamensis 2016: RNAseq of L.panamensis in human macrophages, during infection, in biopsies, and with antimonial treatment.
2018/02/20 RNAseq of L.panamensis: SNP clustering.
2017/09/01 RNAseq of L.panamensis: PBMC Infection Differential Expression.
2017/08/31 RNAseq of L.panamensis: Infection Sample Estimation.
2017/06/21 RNAseq of L.panamensis: Human Macrophage Sample Estimation.
2017/02/06 RNAseq of L.panamensis: Infection Sample Estimation, parasite transcriptome.
2017/02/04 RNAseq of L.panamensis: Infection Sample Estimation, human transcriptome.
2017/02/04 RNAseq of L.panamensis: Parasite Gene Ontology.
2017/02/04 RNAseq of L.panamensis: Human Macrophages Gene Ontology Searches.
2017/02/04 RNAseq of L.panamensis: Parasite Macrophage Sample Estimation.
2017/01/13 RNAseq of L.panamensis: SNP clustering.
2016/12/07 RNAseq of L.panamensis: variancePartition of macrophage parasite data.

DeStefano lab

2021/06/29 Counting RT mutations from illumina sequencing data.
2021/06/21 Counting RT mutations from illumina sequencing data.
2021/06/03 Counting RT mutations from illumina sequencing data.
2021/04/09 Counting RT mutations from illumina sequencing data.
2021/04/07 Counting RT mutations from illumina sequencing data.
2021/04/03 Counting RT mutations from illumina sequencing data.
2021/03/29 Counting RT mutations from illumina sequencing data.
2021/03/18 Counting RT mutations from illumina sequencing data.
2021/01/22 Counting RT mutations from illumina sequencing data.
2021/01/18 Counting RT mutations from illumina sequencing data.
2021/01/16 Counting RT mutations from illumina sequencing data.
2020/09/08 Counting RT mutations from illumina sequencing data.
2020/09/02 Counting RT mutations from illumina sequencing data.
2020/03/12 Counting RT mutations from illumina sequencing data.
2020/01/16 Counting RT mutations from illumina sequencing data.
2020/01/15 Counting RT mutations from illumina sequencing data.
2020/01/12 Counting RT mutations from illumina sequencing data.
2020/01/11 Counting RT mutations from illumina sequencing data.
2020/01/10 Counting RT mutations from illumina sequencing data.
2020/01/09 Counting RT mutations from illumina sequencing data.
2020/01/06 Counting RT mutations from illumina sequencing data.
2019/12/20 Playing with mismatch data.
2019/11/19 A method to estimate RT error rates.

Cruzi lab

2021/03/19 Fernanda’s cool RBP binding experiment.
2021/03/16 Fernanda’s cool RBP binding experiment.
2020/06/29 CL-Brener specific material with Fernanda
2020/06/02 CL-Brener specific material with Fernanda
2020/05/27 CL-Brener specific material with Fernanda
2020/05/26 RNAseq of T.cruzi CL14/CLBr: Sample Estimation
2020/05/20 RNAseq of T.cruzi CL14/CLBr: Sample Estimation
2020/03/27 Some random question from Fernanda.
2020/03/25 T. cruzi human samples with Fernanda: 20200325
2019/09/30 T. cruzi 20190513: Collecting annotation information.
2019/08/22 T. cruzi 20190513: Sample Estimation
2019/08/14 T. cruzi 20190513: Collecting annotation information.
2019/05/29 T. cruzi 20190513: Sample Estimation
2019/05/28 T. cruzi 20190513: Collecting annotation information.
2019/05/17 T. cruzi 20190513: Collecting annotation information.
2019/05/13 T. cruzi 20190513: Collecting annotation information.
2019/03/21 T. cruzi 20190320: Sample Estimation
2018/10/30 L.braziliensis 20170131: RNASeq.
2018/04/23 T.cruzi 2016 CL14/CLBr: Gene Ontology with relaxed fc input.
2018/04/23 T.cruzi 2016 CL14/CLBr: Gene Ontology with a relaxed p-value input.
2018/04/23 T.cruzi 2016 CL14/CLBr: Gene Ontology.
2018/04/23 T.cruzi 2016 CL14/CLBr: Sample Estimation
2018/04/23 T.cruzi 2016 CLBrener/CL14: Collecting annotation information.
2018/04/23 T.cruzi 2016 CL14/CLBr: Gene Ontology.
2018/04/23 T.cruzi 2016 CL14/CLBr: Sample Estimation
2018/04/23 T.cruzi 2016 CLBrener/CL14: KEGG analyses.
2018/04/23 T.cruzi 2016 CL14/CLBr: Differential Expression.
2018/04/23 T.cruzi 2016 CL14/CLBr: Differential Expression.
2018/04/23 T.cruzi 2016 CL14/CLBr: Collecting annotation information.
2018/04/23 T.cruzi CL14/CLBr 2106: Introduction.
2018/04/23 T.cruzi CL14/CLBr 2016: preprocessing raw data.
2018/04/23 T.cruzi 2015: CL14 vs. CLBrener
2018/04/02 L.braziliensis 2017: Annotation data.
2018/04/02 L.braziliensis 2017: RNASeq sample preprocessing.
2017/09/06 RNAseq of L.major odd3 vs wt: Differential Expression.
2017/09/06 RNAseq of L.major odd3 vs wt: Sample Estimation.
2017/09/06 RNASeq o L.major odd3 vs. wt: Collecting annotation.

Mycobacterium tuberculosis

2020/07/21 2020 Mtb. analyses.
2020/06/17 Scatter plot of delta/complement DIA SWATH
2020/06/17 Scatter plot of whole complement/delta DIA SWATH
2020/06/17 Scatter plot of delta/wt culture filtrate DIA SWATH
2020/06/17 Scatter plot of culture filtrate delta/wt DIA SWATH
2020/06/17 Scatter plot of whole cell delta/wt DIA SWATH
2020/06/15 20200320 Mtb. analyses.
2020/06/12 20200320 Mtb. analyses.
2020/01/13 plotly
2019/12/10 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/12/09 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/11/15 plotly
2019/10/29 M.tuberculosis 20191021: All Samples OpenSwathWorkFlow/TRIC.
2019/10/22 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/21 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/18 M.tuberculosis 20190801: Whole Cell Samples OpenSwathWorkFlow/TRIC.
2019/10/18 M.tuberculosis 20190801 proteomics: Collecting annotation data.
2019/10/17 M.tuberculosis 20190718 proteomics: Collecting annotation data.
2019/10/17 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2019/08/22 M.tuberculosis 20190718: Most samples! Analyzing data OpenSwathWorkFlow/TRIC.
2019/08/19 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2019/08/19 M.tuberculosis 20190718 proteomics: Preprocessing.
2019/07/31 M.tuberculosis 20190718 proteomics: Preprocessing.
2019/07/01 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/07/01 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/26 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/26 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/26 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/26 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/24 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/24 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/20 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/20 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/20 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/20 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/07 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/07 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/06/07 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/06/07 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/05/22 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/22 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/21 M. tuberculosis 20190327: DIA-Umpire based OpenSWATH workflow.
2019/05/03 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/03 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/02 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/02 Attempt to compare OpenSWATH to EncyclopeDIA.
2019/05/01 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/05/01 M.tuberculosis 20181112: Most samples! Analyzing data from EncyclopeDIA and OpenSwathWorkFlow/TRIC.
2019/04/30 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/30 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/15 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/15 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/12 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/12 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/11 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/04/11 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2019/03/14 Compare different DIA quantification methods.
2019/03/14 Compare different DIA quantification methods.
2018/11/19 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/11/19 M.tuberculosis 20181112: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/11/12 M.tuberculosis 20181112 proteomics: Collecting annotation data.
2018/11/12 M.tuberculosis 20181112 proteomics: Collecting annotation data.
2018/11/07 M.tuberculosis 20180913: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/11/07 M.tuberculosis 20180913: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/10/31 M.tuberculosis 20180913 proteomics: Collecting annotation data.
2018/10/31 M.tuberculosis 20180913 proteomics: Collecting annotation data.
2018/10/26 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2018/10/26 M.tuberculosis 20180913: Preprocessing DIA data with two libraries.
2018/09/11 M.tuberculosis 20180817: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/09/11 M.tuberculosis 20180817: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/09/06 M.tuberculosis 20180817 proteomics: Collecting annotation data.
2018/09/06 M.tuberculosis 20180817 proteomics: Collecting annotation data.
2018/08/16 M.tuberculosis 20180806: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/08/16 M.tuberculosis 20180806: New samples! Analyzing data from OpenSwathWorkFlow/TRIC.
2018/08/06 M.tuberculosis 20180729: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/08/06 M.tuberculosis 20180729: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/07/31 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC (20180720).
2018/07/31 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC (20180720).
2018/06/14 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/06/14 M.tuberculosis 20180611: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/06/14 M.tuberculosis 20180611 proteomics: Collecting annotation data.
2018/06/14 M.tuberculosis 20180611 proteomics: Collecting annotation data.
2018/06/11 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/06/11 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/30 M.tuberculosis 20180530: Preprocessing DIA data with a comet highres library (more samples).
2018/05/30 M.tuberculosis 20180530: Preprocessing DIA data with a comet highres library (more samples).
2018/05/30 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/30 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/17 M.tuberculosis 201805: Preprocessing DIA data with a comet highres library (more samples).
2018/05/17 M.tuberculosis 201805: Preprocessing DIA data with a comet highres library (more samples).
2018/05/17 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/05/17 M.tuberculosis 201805: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/04/27 M.tuberculosis 2018: Compare kallisto and salmon
2018/04/25 M.tuberculosis 2018: Alternative splicing, suppa.
2018/04/20 M.tuberculosis 2018 proteomics: Introduction/TODO list.
2018/04/20 M.tuberculosis 2018 proteomics: Introduction/TODO list.
2018/04/20 M.tuberculosis 2017 proteomics: Annotation data for proteomics analyses (uniprot).
2018/04/20 M.tuberculosis 2017 proteomics: Annotation data for proteomics analyses (uniprot).
2018/04/20 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/20 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/20 M.tuberculosis 2018: Comparing CID and HCD libraries.
2018/04/20 M.tuberculosis 2018: Comparing CID and HCD libraries.
2018/04/19 M.tuberculosis 2016: A small collection of analyses.
2018/04/19 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/19 M.tuberculosis 2017: Evaluating some MS/MS peptide search metrics.
2018/04/18 M.tuberculosis 2018: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/04/18 M.tuberculosis 2018: Analyzing data from OpenSwathWorkFlow/TRIC.
2018/04/18 M.tuberculosis 2018 proteomics: Collecting annotation data.
2018/04/18 M.tuberculosis 2018 proteomics: Collecting annotation data.
2018/04/18 M.tuberculosis 2018: Preprocessing DIA data with a comet highres library.
2018/04/18 M.tuberculosis 2018: Preprocessing DIA data with a comet highres library.
2018/04/09 M.tuberculosis 201711: Evaluating some MS/MS peptide search metrics.
2018/04/09 M.tuberculosis 201711: Evaluating some MS/MS peptide search metrics.
2018/04/04 M.tuberculosis 2017: Collecting annotation data.
2018/03/30 M.tuberculosis 2017: Testing out Proteomics analyses.
2018/03/30 M.tuberculosis 2017: Testing out Proteomics analyses.
2018/03/30 M.tuberculosis 2017: Relative PE protein expression.
2018/03/29 M.tuberculosis splicing 2018: Annotation data.

Angomonas deanei

2020/06/15 Some very old Angomonas deanei data.

Inbar lab

2020/03/13 Looking for other CDS changes between the wt and ko samples

Sanaria

2020/03/13 Looking for other CDS changes between the wt and ko samples

Salloum

2019/12/12 L. tropica analysis

Biomphalaria glabrata

2019/04/17 B. glabrata RNASeq of two samples
2019/04/12 B. glabrata RNASeq of two samples

Dinman lab

2018/06/19 S. cerevisiae 2017: differential expression, merged sample edition (20180606).
2018/06/19 S. cerevisiae sample estimation, merged sample edition (20180606).
2018/06/06 S.cerevisiae 2017: Collecting annotation data (20180606).
2018/03/28 S. cerevisiae 2017: sample estimation.
2018/03/28 S.cerevisiae 2015: Sample Estimation.
2018/03/28 S.cerevisiae 2016: RNAseq analyses.
2018/03/28 S.cerevisiae 2015: Preprocessing RNAseq samples.
2018/03/27 S.cerevisiae 2015: Annotation.
2018/03/26 S.cerevisiae 2017: Combined RNASeq analyses.
2018/03/23 S.cerevisiae 2016: Preprocessing RNAseq samples.
2018/03/23 S.cerevisiae 2017: Collecting annotation data.
2018/03/23 S.cerevisiae 2016: Collecting annotation data.
2018/03/22 S. cerevisiae sample estimation, merged sample edition.
2017/05/22 S. cerevisiae differential expression.
2017/05/22 S. cerevisiae sample estimation.
2017/03/09 Shared data for RNAseq of S.cerevisiae: Annotation data using R’s SacCer package and biomart.
2016/10/09 RNAsequencing of two Saccharomyces cerevisiae strains.
2016/08/01 RNAseq of S.cerevisiae wt/cbf5 mutants.
2016/07/12 RNAseq of S.cerevisiae wt/cbf5 mutants.
2016/05/19 RNAseq of T.cruzi CL-Brener and CL-14.
2016/04/01 rnaseq_cbf5-201603.html
2015/04/13 rnaseq_cbf5.html

Feijo lab

2018/05/17 S.betaceum 201708: sample estimation of genes.
2018/05/17 S.betaceum 201708: sample estimation of transcripts.
2018/05/17 S.betaceum 201708: annotation data of transcripts.
2018/05/17 S.betaceum 2017: Transcript differential expression.
2018/05/17 S.betaceum 201708: combined analyses.
2018/03/30 S.betaceum 201708: annotation data
2018/03/28 201708: Differential expression of Solanum betaceum.

Leishmania mexicana

2018/04/27 L.mexicana 2017: sample estimation of external samples with Maddy.
2018/04/18 L.mexicana 2017: Annotation data.

Pal lab

2018/04/24 I.scapularis 2017: Tick Differential Expression.
2018/04/24 I.scapularis 2017: Tick Sample Estimation.
2018/04/24 I.scapularis 2017: Tick Annotation Information.
2018/04/23 I.scapularis 2017: Infected mouse differential expression.
2018/04/23 I.scapularis 20170703: Infected mice Gene Ontology Searches.
2018/04/23 I.scapularis 2017: Preprocessing raw data.
2018/04/23 I.scapularis 20170614 Introduction and TODO list.
2018/04/23 I.scapularis 20170628: Infected mice annotation information.
2018/04/23 I.scapularis 20170614: Infected mice gene ontology searches.
2018/04/23 I.scapularis 20170614: Infected mice sample estimation.
2018/04/23 I.scapularis 20170614: Infected mice differential expression.
2018/04/23 I.scapularis 20170614: Infected mice annotation information.
2018/04/20 I.scapularis 2016: Initial RNAseq analyses.
2018/03/27 I.scapularis 2017: Mouse Sample Estimation.
2018/03/27 I.scapularis 2017: Infected mice annotation information.

Leishmania major infectome

Sacks lab

2018/04/20 L.major Sacks 2017: Mouse PMN sample preprocessing.
2018/04/20 L.major Sacks 2017: M.musculus differential expression.
2018/04/20 L.major Sacks 2017: M.musculus (un)infected sample estimation.
2018/04/20 L.major Sacks 2017: differential expression of Leishmania samples.
2018/04/17 L. major 2017: differential expression of Mus samples (201803).
2018/04/16 L. major 2017: sample estimation of new Mouse samples (201803).
2018/04/16 L.major 2017: M.musculus annotation data. (201804)
2018/04/16 L. major 2017: differential expression of Leishmania samples (201803).
2018/04/16 L. major 2017: sample estimation of new Leishmania samples (201803).
2018/04/16 L.major 2018: Mouse PMN infection annotations (201804).
2018/04/04 L. major 2017: sample estimation of Leishmania samples.
2018/04/03 L.major 2017: M.musculus annotation data.
2018/04/02 L.major 2018: Mouse PMN infection annotations.

Fenselau lab

2017/09/05 Sample Estimation of M.musculus samples.
2017/09/05 Annotation data used for M.musculus samples.
2017/03/27 Preprocessing M.musculus samples.
2015/11/05 limma_scatter
2015/01/21 exosome.html

Ribosome profiling of Leishmania major

2014/05/31 ribosome_profiling.html