This tree is intended as a re-evaluation of the RNAseq experiments performed using Leishmania amazonensis.
The global configuration variables for this amazonensis analysis are in configuration.html.
The initial import of data is handled by: data_input.html. This includes reading the gff file and count tables.
The first metrics of the data include library sizes, some box plot goodness, etc. This is handled by: initial_metrics.html.
At the current time, this includes every voom/limma/combat invocation, which is a little excessive. It also has some random plots I happened to think of while drinking some tasty beer. data_normalization.html
I did a few cursory tests comparing the various batch removal choices. batch_removal_tests.html. At this point, I believe we will go with the combat adjusted data.
At this point, the final differential expression is performed using limma’s contrasts.fit, eBayes, and toptable. differential_expression.html.