I spent some time playing with cellranger and its various options for treating gex/atac and their combined datatypes. I think it is unlikely that more than ~ 100 cells are likely to be detected in any combination of options. I therefore thought it would be interesting to attempt treating the samples as separate expression/atac datasets and see if I can learn about the state of the experiment from them.
It might prove the case that downloading annotations from biomart does not work, I have been getting a large number of timeouts and failures recently.
rn_biomart <- load_biomart_annotations(species = "rnorvegicus", year = 2022, month = "oct",
symbol_columns = "external_gene_name", overwrite = TRUE)## Using mart: ENSEMBL_MART_ENSEMBL from host: oct2022.archive.ensembl.org.## Unable to perform useDataset, the given dataset is incorrect: rnorvegicus_gene_ensembl.## c("abrachyrhynchus_gene_ensembl", "acalliptera_gene_ensembl", "acarolinensis_gene_ensembl", "acchrysaetos_gene_ensembl", "acitrinellus_gene_ensembl", "amelanoleuca_gene_ensembl", "amexicanus_gene_ensembl", "anancymaae_gene_ensembl", "aocellaris_gene_ensembl", "apercula_gene_ensembl", "aplatyrhynchos_gene_ensembl", "apolyacanthus_gene_ensembl", "applatyrhynchos_gene_ensembl", "atestudineus_gene_ensembl", "bbbison_gene_ensembl", "bgrunniens_gene_ensembl", "bihybrid_gene_ensembl", "bmusculus_gene_ensembl",
## "bmutus_gene_ensembl", "bsplendens_gene_ensembl", "btaurus_gene_ensembl", "cabingdonii_gene_ensembl", "catys_gene_ensembl", "cauratus_gene_ensembl", "ccapucinus_gene_ensembl", "ccarpio_gene_ensembl", "cccarpio_gene_ensembl", "cdromedarius_gene_ensembl", "celegans_gene_ensembl", "cgchok1gshd_gene_ensembl", "cgobio_gene_ensembl", "charengus_gene_ensembl", "chircus_gene_ensembl", "choffmanni_gene_ensembl", "chyarkandensis_gene_ensembl", "cintestinalis_gene_ensembl", "cjacchus_gene_ensembl", "cjaponica_gene_ensembl",
## "clanigera_gene_ensembl", "cldingo_gene_ensembl", "clfamiliaris_gene_ensembl", "clumpus_gene_ensembl", "cmilii_gene_ensembl", "cpbellii_gene_ensembl", "cporcellus_gene_ensembl", "cporosus_gene_ensembl", "csabaeus_gene_ensembl", "csavignyi_gene_ensembl", "csemilaevis_gene_ensembl", "csyrichta_gene_ensembl", "cvariegatus_gene_ensembl", "cwagneri_gene_ensembl", "dclupeoides_gene_ensembl", "dlabrax_gene_ensembl", "dleucas_gene_ensembl", "dmelanogaster_gene_ensembl", "dnovemcinctus_gene_ensembl", "dordii_gene_ensembl",
## "drerio_gene_ensembl", "eaasinus_gene_ensembl", "eburgeri_gene_ensembl", "ecaballus_gene_ensembl", "ecalabaricus_gene_ensembl", "eelectricus_gene_ensembl", "eeuropaeus_gene_ensembl", "elucius_gene_ensembl", "etelfairi_gene_ensembl", "falbicollis_gene_ensembl", "fcatus_gene_ensembl", "fheteroclitus_gene_ensembl", "gaculeatus_gene_ensembl", "gevgoodei_gene_ensembl", "gfortis_gene_ensembl", "ggallus_gene_ensembl", "ggorilla_gene_ensembl", "gmorhua_gene_ensembl", "hburtoni_gene_ensembl", "hcomes_gene_ensembl",
## "hgfemale_gene_ensembl", "hhucho_gene_ensembl", "hsapiens_gene_ensembl", "ipunctatus_gene_ensembl", "itridecemlineatus_gene_ensembl", "jjaculus_gene_ensembl", "kmarmoratus_gene_ensembl", "lafricana_gene_ensembl", "lbergylta_gene_ensembl", "lcalcarifer_gene_ensembl", "lchalumnae_gene_ensembl", "lcrocea_gene_ensembl", "llaticaudata_gene_ensembl", "lleishanense_gene_ensembl", "loculatus_gene_ensembl", "marmatus_gene_ensembl", "mauratus_gene_ensembl", "mcaroli_gene_ensembl", "mdomestica_gene_ensembl",
## "mfascicularis_gene_ensembl", "mgallopavo_gene_ensembl", "mleucophaeus_gene_ensembl", "mlucifugus_gene_ensembl", "mmmarmota_gene_ensembl", "mmonoceros_gene_ensembl", "mmoschiferus_gene_ensembl", "mmulatta_gene_ensembl", "mmurdjan_gene_ensembl", "mmurinus_gene_ensembl", "mmusculus_gene_ensembl", "mnemestrina_gene_ensembl", "mochrogaster_gene_ensembl", "mpahari_gene_ensembl", "mpfuro_gene_ensembl", "mspicilegus_gene_ensembl", "mspretus_gene_ensembl", "mzebra_gene_ensembl", "nbrichardi_gene_ensembl",
## "neugenii_gene_ensembl", "nfurzeri_gene_ensembl", "ngalili_gene_ensembl", "nleucogenys_gene_ensembl", "nnaja_gene_ensembl", "nscutatus_gene_ensembl", "nvison_gene_ensembl", "oanatinus_gene_ensembl", "oarambouillet_gene_ensembl", "oaries_gene_ensembl", "ocuniculus_gene_ensembl", "odegus_gene_ensembl", "ogarnettii_gene_ensembl", "ojavanicus_gene_ensembl", "okisutch_gene_ensembl", "olatipes_gene_ensembl", "omelastigma_gene_ensembl", "omykiss_gene_ensembl", "oniloticus_gene_ensembl", "oprinceps_gene_ensembl",
## "osinensis_gene_ensembl", "otshawytscha_gene_ensembl", "pabelii_gene_ensembl", "panubis_gene_ensembl", "pcapensis_gene_ensembl", "pcatodon_gene_ensembl", "pcinereus_gene_ensembl", "pcoquereli_gene_ensembl", "pformosa_gene_ensembl", "pkingsleyae_gene_ensembl", "platipinna_gene_ensembl", "pleo_gene_ensembl", "pmajor_gene_ensembl", "pmarinus_gene_ensembl", "pmbairdii_gene_ensembl", "pmuralis_gene_ensembl", "pnattereri_gene_ensembl", "pnyererei_gene_ensembl", "ppaniscus_gene_ensembl", "ppardus_gene_ensembl",
## "preticulata_gene_ensembl", "psimus_gene_ensembl", "psinensis_gene_ensembl", "psinus_gene_ensembl", "ptaltaica_gene_ensembl", "ptextilis_gene_ensembl", "ptroglodytes_gene_ensembl", "pvampyrus_gene_ensembl", "rbieti_gene_ensembl", "rferrumequinum_gene_ensembl", "rnorvegicus_gene_ensembl", "rroxellana_gene_ensembl", "saraneus_gene_ensembl", "saurata_gene_ensembl", "sbboliviensis_gene_ensembl", "scanaria_gene_ensembl", "scaustralis_gene_ensembl", "scerevisiae_gene_ensembl", "sdumerili_gene_ensembl",
## "sformosus_gene_ensembl", "sgrahami_gene_ensembl", "shabroptila_gene_ensembl", "sharrisii_gene_ensembl", "sldorsalis_gene_ensembl", "slucioperca_gene_ensembl", "smaximus_gene_ensembl", "smerianae_gene_ensembl", "spartitus_gene_ensembl", "spunctatus_gene_ensembl", "ssalar_gene_ensembl", "ssbamei_gene_ensembl", "ssberkshire_gene_ensembl", "sscrofa_gene_ensembl", "sshampshire_gene_ensembl", "ssjinhua_gene_ensembl", "sslandrace_gene_ensembl", "sslargewhite_gene_ensembl", "ssmeishan_gene_ensembl", "sspietrain_gene_ensembl",
## "ssrongchang_gene_ensembl", "sstibetan_gene_ensembl", "ssusmarc_gene_ensembl", "sswuzhishan_gene_ensembl", "strutta_gene_ensembl", "svulgaris_gene_ensembl", "tbelangeri_gene_ensembl", "tctriunguis_gene_ensembl", "tguttata_gene_ensembl", "tnigroviridis_gene_ensembl", "trubripes_gene_ensembl", "ttruncatus_gene_ensembl", "uamericanus_gene_ensembl", "umaritimus_gene_ensembl", "uparryii_gene_ensembl", "vpacos_gene_ensembl", "vursinus_gene_ensembl", "vvulpes_gene_ensembl", "xmaculatus_gene_ensembl", "xtropicalis_gene_ensembl"
## ), c("Pink-footed goose genes (ASM259213v1)", "Eastern happy genes (fAstCal1.2)", "Green anole genes (AnoCar2.0v2)", "Golden eagle genes (bAquChr1.2)", "Midas cichlid genes (Midas_v5)", "Giant panda genes (ASM200744v2)", "Mexican tetra genes (Astyanax_mexicanus-2.0)", "Ma's night monkey genes (Anan_2.0)", "Clown anemonefish genes (AmpOce1.0)", "Orange clownfish genes (Nemo_v1)", "Mallard genes (ASM874695v1)", "Spiny chromis genes (ASM210954v1)", "Duck genes (CAU_duck1.0)", "Climbing perch genes (fAnaTes1.2)",
## "American bison genes (Bison_UMD1.0)", "Domestic yak genes (LU_Bosgru_v3.0)", "Hybrid - Bos Indicus genes (UOA_Brahman_1)", "Blue whale genes (mBalMus1.v2)", "Wild yak genes (BosGru_v2.0)", "Siamese fighting fish genes (fBetSpl5.2)", "Cow genes (ARS-UCD1.2)", "Abingdon island giant tortoise genes (ASM359739v1)", "Sooty mangabey genes (Caty_1.0)", "Goldfish genes (ASM336829v1)", "Capuchin genes (Cebus_imitator-1.0)", "Common carp genes (common_carp_genome)", "Common carp genes (Cypcar_WagV4.0)", "Arabian camel genes (CamDro2)",
## "Caenorhabditis elegans (PRJNA13758) genes (WBcel235)", "Chinese hamster CHOK1GS genes (CHOK1GS_HDv1)", "Channel bull blenny genes (fCotGob3.1)", "Atlantic herring genes (Ch_v2.0.2)", "Goat genes (ARS1)", "Sloth genes (choHof1)", "Yarkand deer genes (CEY_v1)", "C.intestinalis genes (KH)", "White-tufted-ear marmoset genes (mCalJac1.pat.X)", "Japanese quail genes (Coturnix_japonica_2.0)", "Long-tailed chinchilla genes (ChiLan1.0)", "Dingo genes (ASM325472v1)", "Dog genes (ROS_Cfam_1.0)", "Lumpfish genes (fCycLum1.pri)",
## "Elephant shark genes (Callorhinchus_milii-6.1.3)", "Painted turtle genes (Chrysemys_picta_bellii-3.0.3)", "Guinea Pig genes (Cavpor3.0)", "Australian saltwater crocodile genes (CroPor_comp1)", "Vervet-AGM genes (ChlSab1.1)", "C.savignyi genes (CSAV 2.0)", "Tongue sole genes (Cse_v1.0)", "Tarsier genes (Tarsius_syrichta-2.0.1)", "Sheepshead minnow genes (C_variegatus-1.0)", "Chacoan peccary genes (CatWag_v2_BIUU_UCD)", "Denticle herring genes (fDenClu1.1)", "European seabass genes (dlabrax2021)",
## "Beluga whale genes (ASM228892v3)", "Drosophila melanogaster genes (BDGP6.32)", "Armadillo genes (Dasnov3.0)", "Kangaroo rat genes (Dord_2.0)", "Zebrafish genes (GRCz11)", "Donkey genes (ASM303372v1)", "Hagfish genes (Eburgeri_3.2)", "Horse genes (EquCab3.0)", "Reedfish genes (fErpCal1.1)", "Electric eel genes (Ee_SOAP_WITH_SSPACE)", "Hedgehog genes (eriEur1)", "Northern pike genes (Eluc_v4)", "Lesser hedgehog tenrec genes (TENREC)", "Collared flycatcher genes (FicAlb1.5)", "Cat genes (Felis_catus_9.0)",
## "Mummichog genes (Fundulus_heteroclitus-3.0.2)", "Stickleback genes (BROAD S1)", "Goodes thornscrub tortoise genes (rGopEvg1_v1.p)", "Medium ground-finch genes (GeoFor_1.0)", "Chicken genes (bGalGal1.mat.broiler.GRCg7b)", "Gorilla genes (gorGor4)", "Atlantic cod genes (gadMor3.0)", "Burton's mouthbrooder genes (AstBur1.0)", "Tiger tail seahorse genes (H_comes_QL1_v1)", "Naked mole-rat female genes (HetGla_female_1.0)", "Huchen genes (ASM331708v1)", "Human genes (GRCh38.p13)", "Channel catfish genes (IpCoco_1.2)",
## "Squirrel genes (SpeTri2.0)", "Lesser Egyptian jerboa genes (JacJac1.0)", "Mangrove rivulus genes (ASM164957v1)", "Elephant genes (Loxafr3.0)", "Ballan wrasse genes (BallGen_V1)", "Barramundi perch genes (ASB_HGAPassembly_v1)", "Coelacanth genes (LatCha1)", "Large yellow croaker genes (L_crocea_2.0)", "Blue-ringed sea krait genes (latLat_1.0)", "Leishan spiny toad genes (ASM966780v1)", "Spotted gar genes (LepOcu1)", "Zig-zag eel genes (fMasArm1.2)", "Golden Hamster genes (MesAur1.0)", "Ryukyu mouse genes (CAROLI_EIJ_v1.1)",
## "Opossum genes (ASM229v1)", "Crab-eating macaque genes (Macaca_fascicularis_6.0)", "Turkey genes (Turkey_5.1)", "Drill genes (Mleu.le_1.0)", "Microbat genes (Myoluc2.0)", "Alpine marmot genes (marMar2.1)", "Narwhal genes (NGI_Narwhal_1)", "Siberian musk deer genes (MosMos_v2_BIUU_UCD)", "Macaque genes (Mmul_10)", "Pinecone soldierfish genes (fMyrMur1.1)", "Mouse Lemur genes (Mmur_3.0)", "Mouse genes (GRCm39)", "Pig-tailed macaque genes (Mnem_1.0)", "Prairie vole genes (MicOch1.0)", "Shrew mouse genes (PAHARI_EIJ_v1.1)",
## "Ferret genes (MusPutFur1.0)", "Steppe mouse genes (MUSP714)", "Algerian mouse genes (SPRET_EiJ_v1)", "Zebra mbuna genes (M_zebra_UMD2a)", "Lyretail cichlid genes (NeoBri1.0)", "Wallaby genes (Meug_1.0)", "Turquoise killifish genes (Nfu_20140520)", "Upper Galilee mountains blind mole rat genes (S.galili_v1.0)", "Gibbon genes (Nleu_3.0)", "Indian cobra genes (Nana_v5)", "Mainland tiger snake genes (TS10Xv2-PRI)", "American mink genes (NNQGG.v01)", "Platypus genes (mOrnAna1.p.v1)", "Sheep genes (Oar_rambouillet_v1.0)",
## "Sheep (texel) genes (Oar_v3.1)", "Rabbit genes (OryCun2.0)", "Degu genes (OctDeg1.0)", "Bushbaby genes (OtoGar3)", "Javanese ricefish genes (OJAV_1.1)", "Coho salmon genes (Okis_V2)", "Japanese medaka HdrR genes (ASM223467v1)", "Indian medaka genes (Om_v0.7.RACA)", "Rainbow trout genes (USDA_OmykA_1.1)", "Nile tilapia genes (O_niloticus_UMD_NMBU)", "Pika genes (OchPri2.0-Ens)", "Chinese medaka genes (ASM858656v1)", "Chinook salmon genes (Otsh_v1.0)", "Sumatran orangutan genes (Susie_PABv2)", "Olive baboon genes (Panubis1.0)",
## "Hyrax genes (proCap1)", "Sperm whale genes (ASM283717v2)", "Koala genes (phaCin_unsw_v4.1)", "Coquerel's sifaka genes (Pcoq_1.0)", "Amazon molly genes (Poecilia_formosa-5.1.2)", "Paramormyrops kingsleyae genes (PKINGS_0.1)", "Sailfin molly genes (P_latipinna-1.0)", "Lion genes (PanLeo1.0)", "Great Tit genes (Parus_major1.1)", "Lamprey genes (Pmarinus_7.0)", "Northern American deer mouse genes (HU_Pman_2.1)", "Common wall lizard genes (PodMur_1.0)", "Red-bellied piranha genes (Pygocentrus_nattereri-1.0.2)",
## "Makobe Island cichlid genes (PunNye1.0)", "Bonobo genes (panpan1.1)", "Leopard genes (PanPar1.0)", "Guppy genes (Guppy_female_1.0_MT)", "Greater bamboo lemur genes (Prosim_1.0)", "Chinese softshell turtle genes (PelSin_1.0)", "Vaquita genes (mPhoSin1.pri)", "Tiger genes (PanTig1.0)", "Eastern brown snake genes (EBS10Xv2-PRI)", "Chimpanzee genes (Pan_tro_3.0)", "Megabat genes (pteVam1)", "Black snub-nosed monkey genes (ASM169854v1)", "Greater horseshoe bat genes (mRhiFer1_v1.p)", "Rat genes (mRatBN7.2)",
## "Golden snub-nosed monkey genes (Rrox_v1)", "Shrew genes (sorAra1)", "Gilthead seabream genes (fSpaAur1.1)", "Bolivian squirrel monkey genes (SaiBol1.0)", "Common canary genes (SCA1)", "African ostrich genes (ASM69896v1)", "Saccharomyces cerevisiae genes (R64-1-1)", "Greater amberjack genes (Sdu_1.0)", "Asian bonytongue genes (fSclFor1.1)", "Golden-line barbel genes (SAMN03320097.WGS_v1.1)", "Kakapo genes (bStrHab1_v1.p)", "Tasmanian devil genes (mSarHar1.11)", "Yellowtail amberjack genes (Sedor1)",
## "Pike-perch genes (SLUC_FBN_1)", "Turbot genes (ASM1334776v1)", "Argentine black and white tegu genes (HLtupMer3)", "Bicolor damselfish genes (Stegastes_partitus-1.0.2)", "Tuatara genes (ASM311381v1)", "Atlantic salmon genes (Ssal_v3.1)", "Pig - Bamei genes (Bamei_pig_v1)", "Pig - Berkshire genes (Berkshire_pig_v1)", "Pig genes (Sscrofa11.1)", "Pig - Hampshire genes (Hampshire_pig_v1)", "Pig - Jinhua genes (Jinhua_pig_v1)", "Pig - Landrace genes (Landrace_pig_v1)", "Pig - Largewhite genes (Large_White_v1)",
## "Pig - Meishan genes (Meishan_pig_v1)", "Pig - Pietrain genes (Pietrain_pig_v1)", "Pig - Rongchang genes (Rongchang_pig_v1)", "Pig - Tibetan genes (Tibetan_Pig_v2)", "Pig USMARC genes (USMARCv1.0)", "Pig - Wuzhishan genes (minipig_v1.0)", "Brown trout genes (fSalTru1.1)", "Eurasian red squirrel genes (mSciVul1.1)", "Tree Shrew genes (tupBel1)", "Three-toed box turtle genes (T_m_triunguis-2.0)", "Zebra finch genes (bTaeGut1_v1.p)", "Tetraodon genes (TETRAODON 8.0)", "Fugu genes (fTakRub1.2)", "Dolphin genes (turTru1)",
## "American black bear genes (ASM334442v1)", "Polar bear genes (UrsMar_1.0)", "Arctic ground squirrel genes (ASM342692v1)", "Alpaca genes (vicPac1)", "Common wombat genes (bare-nosed_wombat_genome_assembly)", "Red fox genes (VulVul2.2)", "Platyfish genes (X_maculatus-5.0-male)", "Tropical clawed frog genes (UCB_Xtro_10.0)"), c("ASM259213v1", "fAstCal1.2", "AnoCar2.0v2", "bAquChr1.2", "Midas_v5", "ASM200744v2", "Astyanax_mexicanus-2.0", "Anan_2.0", "AmpOce1.0", "Nemo_v1", "ASM874695v1", "ASM210954v1", "CAU_duck1.0", "fAnaTes1.2", "Bison_UMD1.0", "LU_Bosgru_v3.0", "UOA_Brahman_1", "mBalMus1.v2", "BosGru_v2.0", "fBetSpl5.2", "ARS-UCD1.2", "ASM359739v1", "Caty_1.0", "ASM336829v1", "Cebus_imitator-1.0", "common_carp_genome", "Cypcar_WagV4.0", "CamDro2", "WBcel235", "CHOK1GS_HDv1", "fCotGob3.1", "Ch_v2.0.2", "ARS1", "choHof1",
## "CEY_v1", "KH", "mCalJac1.pat.X", "Coturnix_japonica_2.0", "ChiLan1.0", "ASM325472v1", "ROS_Cfam_1.0", "fCycLum1.pri", "Callorhinchus_milii-6.1.3", "Chrysemys_picta_bellii-3.0.3", "Cavpor3.0", "CroPor_comp1", "ChlSab1.1", "CSAV 2.0", "Cse_v1.0", "Tarsius_syrichta-2.0.1", "C_variegatus-1.0", "CatWag_v2_BIUU_UCD", "fDenClu1.1", "dlabrax2021", "ASM228892v3", "BDGP6.32", "Dasnov3.0", "Dord_2.0", "GRCz11", "ASM303372v1", "Eburgeri_3.2", "EquCab3.0", "fErpCal1.1", "Ee_SOAP_WITH_SSPACE", "eriEur1", "Eluc_v4",
## "TENREC", "FicAlb1.5", "Felis_catus_9.0", "Fundulus_heteroclitus-3.0.2", "BROAD S1", "rGopEvg1_v1.p", "GeoFor_1.0", "bGalGal1.mat.broiler.GRCg7b", "gorGor4", "gadMor3.0", "AstBur1.0", "H_comes_QL1_v1", "HetGla_female_1.0", "ASM331708v1", "GRCh38.p13", "IpCoco_1.2", "SpeTri2.0", "JacJac1.0", "ASM164957v1", "Loxafr3.0", "BallGen_V1", "ASB_HGAPassembly_v1", "LatCha1", "L_crocea_2.0", "latLat_1.0", "ASM966780v1", "LepOcu1", "fMasArm1.2", "MesAur1.0", "CAROLI_EIJ_v1.1", "ASM229v1", "Macaca_fascicularis_6.0",
## "Turkey_5.1", "Mleu.le_1.0", "Myoluc2.0", "marMar2.1", "NGI_Narwhal_1", "MosMos_v2_BIUU_UCD", "Mmul_10", "fMyrMur1.1", "Mmur_3.0", "GRCm39", "Mnem_1.0", "MicOch1.0", "PAHARI_EIJ_v1.1", "MusPutFur1.0", "MUSP714", "SPRET_EiJ_v1", "M_zebra_UMD2a", "NeoBri1.0", "Meug_1.0", "Nfu_20140520", "S.galili_v1.0", "Nleu_3.0", "Nana_v5", "TS10Xv2-PRI", "NNQGG.v01", "mOrnAna1.p.v1", "Oar_rambouillet_v1.0", "Oar_v3.1", "OryCun2.0", "OctDeg1.0", "OtoGar3", "OJAV_1.1", "Okis_V2", "ASM223467v1", "Om_v0.7.RACA", "USDA_OmykA_1.1",
## "O_niloticus_UMD_NMBU", "OchPri2.0-Ens", "ASM858656v1", "Otsh_v1.0", "Susie_PABv2", "Panubis1.0", "proCap1", "ASM283717v2", "phaCin_unsw_v4.1", "Pcoq_1.0", "Poecilia_formosa-5.1.2", "PKINGS_0.1", "P_latipinna-1.0", "PanLeo1.0", "Parus_major1.1", "Pmarinus_7.0", "HU_Pman_2.1", "PodMur_1.0", "Pygocentrus_nattereri-1.0.2", "PunNye1.0", "panpan1.1", "PanPar1.0", "Guppy_female_1.0_MT", "Prosim_1.0", "PelSin_1.0", "mPhoSin1.pri", "PanTig1.0", "EBS10Xv2-PRI", "Pan_tro_3.0", "pteVam1", "ASM169854v1", "mRhiFer1_v1.p",
## "mRatBN7.2", "Rrox_v1", "sorAra1", "fSpaAur1.1", "SaiBol1.0", "SCA1", "ASM69896v1", "R64-1-1", "Sdu_1.0", "fSclFor1.1", "SAMN03320097.WGS_v1.1", "bStrHab1_v1.p", "mSarHar1.11", "Sedor1", "SLUC_FBN_1", "ASM1334776v1", "HLtupMer3", "Stegastes_partitus-1.0.2", "ASM311381v1", "Ssal_v3.1", "Bamei_pig_v1", "Berkshire_pig_v1", "Sscrofa11.1", "Hampshire_pig_v1", "Jinhua_pig_v1", "Landrace_pig_v1", "Large_White_v1", "Meishan_pig_v1", "Pietrain_pig_v1", "Rongchang_pig_v1", "Tibetan_Pig_v2", "USMARCv1.0", "minipig_v1.0",
## "fSalTru1.1", "mSciVul1.1", "tupBel1", "T_m_triunguis-2.0", "bTaeGut1_v1.p", "TETRAODON 8.0", "fTakRub1.2", "turTru1", "ASM334442v1", "UrsMar_1.0", "ASM342692v1", "vicPac1", "bare-nosed_wombat_genome_assembly", "VulVul2.2", "X_maculatus-5.0-male", "UCB_Xtro_10.0")## Error in `martCheck()`:
## ! You must provide a valid Mart object. To create a Mart object use the function: useMart. Check ?useMart for more information.## Returning a df with 26 columns and 1426516 rows.## Error:
## ! object 'rn_biomart' not foundMy annotation collection tool is unaware of atac data. I think therefore I will try runing it and just see what happens.
sample_sheet <- "sample_sheets/all_samples.xlsx"
rn_meta <- gather_preprocessing_metadata(sample_sheet,
species = "rnorvegicus_7.2_107")## Did not find the condition column in the sample sheet.## Filling it in as undefined.## Did not find the batch column in the sample sheet.## Filling it in as undefined.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## Writing new metadata to: sample_sheets/all_samples_modified.xlsx## Deleting the file sample_sheets/all_samples_modified.xlsx before writing the tables.It fails utterly.
rn_se <- create_se(sample_sheet, gene_info = rn_annot, file_column = "gex_count_table") %>%
set_conditions(fact = "treatment") %>%
set_batches(fact = "replicate")## Reading the sample metadata.## Did not find the condition column in the sample sheet.## Filling it in as undefined.## Did not find the batch column in the sample sheet.## Filling it in as undefined.## Checking the state of the condition column.## Checking the state of the batch column.## Checking the condition factor.## The sample definitions comprises: 8 rows(samples) and 8 columns(metadata fields).## Warning in create_se(sample_sheet, gene_info = rn_annot, file_column =
## "gex_count_table"): Some samples were removed when cross referencing the samples
## against the count data.## Error in `h()`:
## ! error in evaluating the argument 'exp' in selecting a method for function 'set_batches': error in evaluating the argument 'exp' in selecting a method for function 'set_conditions': object 'rn_annot' not found## Error in `h()`:
## ! error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'rn_se' not found## Error:
## ! object 'rn_libsize' not found## png
## 2## Error:
## ! object 'rn_libsize' not found## Error in `h()`:
## ! error in evaluating the argument 'data' in selecting a method for function 'plot_nonzero': object 'rn_se' not found## Error:
## ! object 'rn_nz' not found## png
## 2## Error:
## ! object 'rn_nz' not found## Error in `h()`:
## ! error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'rn_se' not found## Error in `h()`:
## ! error in evaluating the argument 'input_data' in selecting a method for function 'plot_heatmap': object 'rn_norm' not found## Error:
## ! object 'rn_disheat' not found## png
## 2## Error:
## ! object 'rn_disheat' not found## Error in `h()`:
## ! error in evaluating the argument 'input_data' in selecting a method for function 'plot_heatmap': object 'rn_norm' not found## Error:
## ! object 'rn_corheat' not found## png
## 2## Error:
## ! object 'rn_corheat' not found## Error in `h()`:
## ! error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'rn_norm' not found## Error:
## ! object 'rn_npca' not found## png
## 2## Error:
## ! object 'rn_npca' not found## Error in `h()`:
## ! error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'rn_se' not found## Error in `h()`:
## ! error in evaluating the argument 'data' in selecting a method for function 'plot_pca': object 'rn_nb' not found## Error:
## ! object 'rn_nbpca' not found## png
## 2## Error:
## ! object 'rn_nbpca' not foundLet us pull the rpkm values of 1,2 and 3,4 and explicitly compare them and see if groups of noteworthy genes appear.
rn_rpkm <- normalize(rn_se, transform = "log2", convert = "rpkm", filter = TRUE, norm = "quant",
length_column = "cds_length")## Error in `h()`:
## ! error in evaluating the argument 'object' in selecting a method for function 'normalize': object 'rn_se' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'assay': object 'rn_rpkm' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'assay': object 'rn_rpkm' not foundpaired_mtrx <- data.frame(row.names = rownames(assay(rn_rpkm)),
"first_two" = first_two,
"second_two" = second_two)## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'rownames': error in evaluating the argument 'x' in selecting a method for function 'assay': object 'rn_rpkm' not found## Error:
## ! object 'paired_mtrx' not found## Error:
## ! object 'paired_mtrx' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'paired_mtrx' not found## Error:
## ! object 'paired_mtrx' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'paired_mtrx' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'merge': error in evaluating the argument 'x' in selecting a method for function 'rowData': object 'rn_se' not found## Error:
## ! object 'paired_mtrx_annotated' not found## Error:
## ! object 'paired_mtrx_annotated' not found## Error in `h()`:
## ! error in evaluating the argument 'data' in selecting a method for function 'write_xlsx': object 'paired_mtrx_annotated' not found## Error:
## ! object 'first_higher_oxy' not found## Error:
## ! object 'second_higher_oxy' not found## Error:
## ! object 'first_higher_oxy' not found## Error:
## ! object 'paired_mtrx' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'paired_mtrx' not found## Error:
## ! object 'paired_mtrx' not found## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'paired_mtrx' not found## Error:
## ! object 'first_higher_saline' not found## Error:
## ! object 'second_higher_saline' not found## Error:
## ! object 'first_higher_saline' not foundpairs <- all_pairwise(rn_se, model_svs = "svaseq", force = TRUE,
model_fstring = "~ 0 + condition", filter = TRUE)## Error in `h()`:
## ! error in evaluating the argument 'x' in selecting a method for function 'colData': object 'rn_se' not found## function (x, ...)
## UseMethod("pairs")
## <bytecode: 0x55c8f1c08158>
## <environment: namespace:graphics>## Deleting the file excel/pairs.xlsx before writing the tables.## Error in `apr[[q]]`:
## ! object of type 'closure' is not subsettable## function (..., exclude = if (useNA == "no") c(NA, NaN), useNA = c("no",
## "ifany", "always"), dnn = list.names(...), deparse.level = 1)
## {
## list.names <- function(...) {
## l <- as.list(substitute(list(...)))[-1L]
## if (length(l) == 1L && is.list(..1) && !is.null(nm <- names(..1)))
## return(nm)
## nm <- names(l)
## fixup <- if (is.null(nm))
## seq_along(l)
## else nm == ""
## dep <- vapply(l[fixup], function(x) switch(deparse.level +
## 1, "", if (is.symbol(x)) as.character(x) else "",
## deparse(x, nlines = 1)[1L]), "")
## if (is.null(nm))
## dep
## else {
## nm[fixup] <- dep
## nm
## }
## }
## miss.use <- missing(useNA)
## miss.exc <- missing(exclude)
## useNA <- if (miss.use && !miss.exc && !match(NA, exclude,
## nomatch = 0L))
## "ifany"
## else match.arg(useNA)
## doNA <- useNA != "no"
## if (!miss.use && !miss.exc && doNA && match(NA, exclude,
## nomatch = 0L))
## warning("'exclude' containing NA and 'useNA' != \"no\"' are a bit contradicting")
## args <- list(...)
## if (length(args) == 1L && is.list(args[[1L]])) {
## args <- args[[1L]]
## if (length(dnn) != length(args))
## dnn <- paste(dnn[1L], seq_along(args), sep = ".")
## }
## if (!length(args))
## stop("nothing to tabulate")
## bin <- 0L
## lens <- NULL
## dims <- integer()
## pd <- 1L
## dn <- NULL
## for (a in args) {
## if (is.null(lens))
## lens <- length(a)
## else if (length(a) != lens)
## stop("all arguments must have the same length")
## fact.a <- is.factor(a)
## if (doNA)
## aNA <- anyNA(a)
## if (!fact.a) {
## a0 <- a
## op <- options(warn = 2)
## on.exit(options(op))
## a <- factor(a, exclude = exclude)
## options(op)
## }
## add.na <- doNA
## if (add.na) {
## ifany <- (useNA == "ifany")
## anNAc <- anyNA(a)
## add.na <- if (!ifany || anNAc) {
## ll <- levels(a)
## if (add.ll <- !anyNA(ll)) {
## ll <- c(ll, NA)
## TRUE
## }
## else if (!ifany && !anNAc)
## FALSE
## else TRUE
## }
## else FALSE
## }
## if (add.na)
## a <- factor(a, levels = ll, exclude = NULL)
## else ll <- levels(a)
## a <- as.integer(a)
## if (fact.a && !miss.exc) {
## ll <- ll[keep <- which(match(ll, exclude, nomatch = 0L) ==
## 0L)]
## a <- match(a, keep)
## }
## else if (!fact.a && add.na) {
## if (ifany && !aNA && add.ll) {
## ll <- ll[!is.na(ll)]
## is.na(a) <- match(a0, c(exclude, NA), nomatch = 0L) >
## 0L
## }
## else {
## is.na(a) <- match(a0, exclude, nomatch = 0L) >
## 0L
## }
## }
## nl <- length(ll)
## dims <- c(dims, nl)
## if (prod(dims) > .Machine$integer.max)
## stop("attempt to make a table with >= 2^31 elements")
## dn <- c(dn, list(ll))
## bin <- bin + pd * (a - 1L)
## pd <- pd * nl
## }
## names(dn) <- dnn
## bin <- bin[!is.na(bin)]
## if (length(bin))
## bin <- bin + 1L
## y <- array(tabulate(bin, pd), dims, dimnames = dn)
## class(y) <- "table"
## y
## }
## <bytecode: 0x55c8f63a4bf0>
## <environment: namespace:base>## Deleting the file excel/sig.xlsx before writing the tables.## Error in `combined[["contrast_list"]]`:
## ! object of type 'closure' is not subsettable## Error:
## ! object 'sig' not foundLimma volcano plot
In theory, the column ‘external_gene_name’ should provide reasonable genenames, but I am having some troubles extracting it from ensembl.
## Error in `table[["plots"]]`:
## ! object of type 'closure' is not subsettable## png
## 2## Error in `table[["plots"]]`:
## ! object of type 'closure' is not subsettable## Error:
## ! object 'sig' not found## Error:
## ! object 'ups' not found## Error:
## ! object 'sig' not found## Error:
## ! object 'downs' not found## Error:
## ! object 'ups' not found## Error:
## ! object 'gp_up' not found## NULL## png
## 2## Error:
## ! object 'gp_up' not found## NULL## png
## 2Given my lack of experience with ATAC data, I am currently using
as a guide.
## Loading required package: BiocGenerics## Loading required package: generics##
## Attaching package: 'generics'## The following objects are masked from 'package:base':
##
## as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
## setequal, union##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:hpgltools':
##
## annotation<-, conditions, conditions<-, IQR, mad, sd, var, xtabs## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, is.unsorted, lapply, Map, mapply, match, mget, order, paste,
## pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
## rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max,
## which.min## Loading required package: S4Vectors## Loading required package: stats4##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:utils':
##
## findMatches## The following objects are masked from 'package:base':
##
## expand.grid, I, unname## Loading required package: BSgenome## Loading required package: IRanges##
## Attaching package: 'IRanges'## The following object is masked from 'package:hpgltools':
##
## trim## Loading required package: Seqinfo## Loading required package: GenomicRanges## Loading required package: Biostrings## Loading required package: XVector##
## Attaching package: 'Biostrings'## The following object is masked from 'package:base':
##
## strsplit## Loading required package: BiocIO##
## Attaching package: 'BiocIO'## The following object is masked from 'package:reticulate':
##
## import## Loading required package: rtracklayer## Loading required package: GenomicFeatures## Loading required package: AnnotationDbi## Loading required package: Biobase## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with 'browseVignettes()'.
## To cite Bioconductor, see 'citation("Biobase")', and for packages
## 'citation("pkgname")'.##
## Attaching package: 'Biobase'## The following object is masked from 'package:hpgltools':
##
## noteslibrary(ChIPpeakAnno)
library(Rsamtools)
bam_outputs <- c(
"preprocessing/1_saline_atac/outputs/40hisat_rnorvegicus_norway_grcr8/rnorvegicus_norway_grcr8_genome-paired.bam",
"preprocessing/2_oxycodone_atac/outputs/40hisat_rnorvegicus_norway_grcr8/rnorvegicus_norway_grcr8_genome-paired.bam",
"preprocessing/3_saline_atac/outputs/40hisat_rnorvegicus_norway_grcr8/rnorvegicus_norway_grcr8_genome-paired.bam",
"preprocessing/4_oxycodone_atac/outputs/40hisat_rnorvegicus_norway_grcr8/rnorvegicus_norway_grcr8_genome-paired.bam")
bam_qc <- bamQC(bam_outputs[1], outPath = NULL)
possibleTag <- combn(LETTERS, 2)
possibleTag <- c(paste0(possibleTag[1, ], possibleTag[2, ]),
paste0(possibleTag[2, ], possibleTag[1, ]))
## This seems a bit stupid? I already know what the primary sam tags are, should I not just
## have a list with their names and meanings?
bamTop100 <- scanBam(BamFile(bam_outputs[1], yieldSize = 100),
param = ScanBamParam(tag = possibleTag))[[1]]$tag
tags <- names(bamTop100)[lengths(bamTop100)>0]
tags## [1] "AS" "MD" "XG" "NH" "NM" "XM" "XN" "XO" "YS" "ZS" "YT"gal = readBamFile(bam_outputs[1], tag = tags, asMates = TRUE, bigFile = TRUE)
out_dir <- "preprocessing/1_saline_atac/outputs/99atac_qc"
dir.create(out_dir, recursive = TRUE)## Warning in dir.create(out_dir, recursive = TRUE):
## 'preprocessing/1_saline_atac/outputs/99atac_qc' already existsshifted_bam <- file.path(out_dir, "shifted.bam")
gal1 = shiftGAlignmentsList(gal, outbam = shifted_bam)## | | | 0% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 7% | |====== | 8% | |======= | 9% | |======= | 10% | |======== | 11% | |========= | 11% | |========= | 12% | |========== | 13% | |========== | 14% | |=========== | 15% | |============ | 16% | |============= | 17% | |============== | 18% | |============== | 19% | |=============== | 20% | |================ | 21% | |================= | 22% | |================= | 23% | |================== | 24% | |================== | 25% | |=================== | 25% | |==================== | 26% | |==================== | 27% | |===================== | 28% | |====================== | 29% | |====================== | 30% | |======================= | 30% | |======================= | 31% | |======================== | 32% | |========================= | 33% | |========================= | 34% | |========================== | 34% | 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|======================================================================= | 94% | |======================================================================= | 95% | |======================================================================== | 96% | |========================================================================= | 97% | |========================================================================= | 98% | |========================================================================== | 98% | |========================================================================== | 99% | |===========================================================================| 100%R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats4, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: Rsamtools(v.2.26.0), ChIPpeakAnno(v.3.44.0), TxDb.Rnorvegicus.UCSC.rn7.refGene(v.3.15.0), GenomicFeatures(v.1.62.0), AnnotationDbi(v.1.72.0), Biobase(v.2.70.0), BSgenome.Rnorvegicus.UCSC.rn7(v.1.4.3), BSgenome(v.1.78.0), rtracklayer(v.1.70.1), BiocIO(v.1.20.0), Biostrings(v.2.78.0), XVector(v.0.50.0), GenomicRanges(v.1.62.1), Seqinfo(v.1.0.0), IRanges(v.2.44.0), ATACseqQC(v.1.34.0), S4Vectors(v.0.48.1), BiocGenerics(v.0.56.0), generics(v.0.1.4), hpgltools(v.2026.03), testthat(v.3.3.2) and reticulate(v.1.45.0)
loaded via a namespace (and not attached): R.methodsS3(v.1.8.2), dichromat(v.2.0-0.1), GSEABase(v.1.72.0), progress(v.1.2.3), PROPER(v.1.42.0), HDF5Array(v.1.38.0), restez(v.2.1.5), vctrs(v.0.7.2), ggtangle(v.0.1.1), digest(v.0.6.39), png(v.0.1-9), corpcor(v.1.6.10), ggrepel(v.0.9.8), MASS(v.7.3-65), fontLiberation(v.0.1.0), reshape2(v.1.4.5), httpuv(v.1.6.17), foreach(v.1.5.2), qvalue(v.2.42.0), withr(v.3.0.2), xfun(v.0.57), ggfun(v.0.2.0), ellipsis(v.0.3.3), survival(v.3.8-6), memoise(v.2.0.1), clusterProfiler(v.4.18.4), gson(v.0.1.0), systemfonts(v.1.3.2), tidytree(v.0.4.7), gtools(v.3.9.5), R.oo(v.1.27.1), prettyunits(v.1.2.0), KEGGREST(v.1.50.0), promises(v.1.5.0), otel(v.0.2.0), httr(v.1.4.8), restfulr(v.0.0.16), rhdf5filters(v.1.22.0), rhdf5(v.2.55.13), rstudioapi(v.0.18.0), UCSC.utils(v.1.6.1), DOSE(v.4.4.0), curl(v.7.0.0), h5mread(v.1.2.1), randomForest(v.4.7-1.2), polyclip(v.1.10-7), SparseArray(v.1.10.10), RBGL(v.1.86.0), ade4(v.1.7-24), xtable(v.1.8-8), stringr(v.1.6.0), desc(v.1.4.3), evaluate(v.1.0.5), S4Arrays(v.1.10.1), BiocFileCache(v.3.0.0), hms(v.1.1.4), filelock(v.1.0.3), polynom(v.1.4-1), VennDiagram(v.1.8.2), magrittr(v.2.0.5), later(v.1.4.8), ggtree(v.4.0.5), lattice(v.0.22-9), genefilter(v.1.92.0), XML(v.3.99-0.23), cowplot(v.1.2.0), matrixStats(v.1.5.0), pillar(v.1.11.1), nlme(v.3.1-169), iterators(v.1.0.14), pwalign(v.1.6.0), caTools(v.1.18.3), compiler(v.4.5.1), stringi(v.1.8.7), minqa(v.1.2.8), SummarizedExperiment(v.1.40.0), devtools(v.2.5.0), GenomicAlignments(v.1.46.0), plyr(v.1.8.9), crayon(v.1.5.3), abind(v.1.4-8), gridGraphics(v.0.5-1), locfit(v.1.5-9.12), bit(v.4.6.0), dplyr(v.1.2.1), fastmatch(v.1.1-8), codetools(v.0.2-20), bslib(v.0.10.0), plotly(v.4.12.0), multtest(v.2.66.0), remaCor(v.0.0.20), mime(v.0.13), splines(v.4.5.1), Rcpp(v.1.1.1), tidydr(v.0.0.6), dbplyr(v.2.5.2), knitr(v.1.51), blob(v.1.3.0), seqLogo(v.1.76.0), BiocVersion(v.3.22.0), AnnotationFilter(v.1.34.0), lme4(v.2.0-1), fs(v.2.0.1), Rdpack(v.2.6.6), pkgbuild(v.1.4.8), openxlsx(v.4.2.8.1), ggplotify(v.0.1.3), tibble(v.3.3.1), Matrix(v.1.7-5), statmod(v.1.5.1), fANCOVA(v.0.6-1), tweenr(v.2.0.3), pkgconfig(v.2.0.3), tools(v.4.5.1), cachem(v.1.1.0), RhpcBLASctl(v.0.23-42), rbibutils(v.2.4.1), cigarillo(v.1.0.0), RSQLite(v.2.4.6), viridisLite(v.0.4.3), DBI(v.1.3.0), numDeriv(v.2016.8-1.1), fastmap(v.1.2.0), rmarkdown(v.2.31), scales(v.1.4.0), grid(v.4.5.1), usethis(v.3.2.1), AnnotationHub(v.4.0.0), broom(v.1.0.12), sass(v.0.4.10), patchwork(v.1.3.2), BiocManager(v.1.30.27), graph(v.1.88.1), varhandle(v.2.0.6), farver(v.2.1.2), reformulas(v.0.4.4), aod(v.1.3.3), scatterpie(v.0.2.6), mgcv(v.1.9-4), yaml(v.2.3.12), MatrixGenerics(v.1.22.0), cli(v.3.6.5), purrr(v.1.2.1), lifecycle(v.1.0.5), mvtnorm(v.1.3-6), lambda.r(v.1.2.4), sessioninfo(v.1.2.3), backports(v.1.5.1), BiocParallel(v.1.44.0), annotate(v.1.88.0), gtable(v.0.3.6), rjson(v.0.2.23), parallel(v.4.5.1), ape(v.5.8-1), limma(v.3.66.0), jsonlite(v.2.0.0), edgeR(v.4.8.2), TFBSTools(v.1.48.0), bitops(v.1.0-9), ggplot2(v.4.0.2), bit64(v.4.6.0-1), brio(v.1.1.5), yulab.utils(v.0.2.4), zip(v.2.3.3), futile.options(v.1.0.1), jquerylib(v.0.1.4), GOSemSim(v.2.36.0), R.utils(v.2.13.0), pbkrtest(v.0.5.5), lazyeval(v.0.2.3), pander(v.0.6.6), shiny(v.1.13.0), htmltools(v.0.5.9), enrichplot(v.1.30.5), GO.db(v.3.22.0), rappdirs(v.0.3.4), formatR(v.1.14), ensembldb(v.2.34.0), glue(v.1.8.0), TFMPvalue(v.1.0.0), GenomicScores(v.2.22.0), httr2(v.1.2.2), gdtools(v.0.5.0), RCurl(v.1.98-1.18), InteractionSet(v.1.38.0), rprojroot(v.2.1.1), treeio(v.1.34.0), motifStack(v.1.54.0), futile.logger(v.1.4.9), EnvStats(v.3.1.0), boot(v.1.3-32), preseqR(v.4.0.0), universalmotif(v.1.28.0), igraph(v.2.2.3), variancePartition(v.1.40.2), R6(v.2.6.1), sva(v.3.58.0), tidyr(v.1.3.2), DESeq2(v.1.50.2), ggiraph(v.0.9.6), gplots(v.3.3.0), cluster(v.2.1.8.2), pkgload(v.1.5.1), Rhdf5lib(v.1.32.0), regioneR(v.1.42.0), aplot(v.0.2.9), GenomeInfoDb(v.1.46.2), DirichletMultinomial(v.1.52.0), nloptr(v.2.2.1), DelayedArray(v.0.36.1), tidyselect(v.1.2.1), ProtGenerics(v.1.42.0), ggforce(v.0.5.0), xml2(v.1.5.2), fontBitstreamVera(v.0.1.1), KernSmooth(v.2.23-26), S7(v.0.2.1), fontquiver(v.0.2.1), data.table(v.1.18.2.1), htmlwidgets(v.1.6.4), fgsea(v.1.36.2), RColorBrewer(v.1.1-3), biomaRt(v.2.66.2), rlang(v.1.2.0), lmerTest(v.3.2-1) and ggnewscale(v.0.5.2)
## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset 35ca3028a5bd7bb6b3b242189a1ec1d2abf7f425## This is hpgltools commit: Mon Apr 20 11:38:32 2026 -0400: 35ca3028a5bd7bb6b3b242189a1ec1d2abf7f425this_save <- paste0(gsub(pattern = "\\.Rmd", replace = "", x = rmd_file), "-v", ver, ".rda.xz")
message("Saving to ", this_save)## Saving to index-v20260421.rda.xz