Files in soderling-lab/geneLists

tools for mapping gene identifiers and a collection of gene lists in a universal format

R/data_alsgene.R R/data_alsodgene.R R/data_alzgene.R R/data_arrabroadwave3ASD.R R/data_biesemann2014sortedsynaptosomes.R R/data_boyken2013presynapse.R R/data_chen2014AMPARs.R R/data_cheng2006PSD.R R/data_ciPSD.R R/data_collins2005phospho.R R/data_collins2006PSD.R R/data_corum.R R/data_deligt2012ID.R R/data_derubeis2014ASD.R R/data_disgeneDBD.R R/data_disgeneLSD.R R/data_disgeneNDD.R R/data_dosemeci2007PSD95proteome.R R/data_ePSD.R R/data_emptyDataset.R R/data_fromer2014dbd.R R/data_fromer2014schz.R R/data_g2pDBD.R R/data_geisingerDBD.R R/data_girard2011SZ.R R/data_gulsuner2013SZ.R R/data_han2013shank3proteome.R R/data_hlgd.R R/data_hshallmark.R R/data_iPSD.R R/data_iossifov2012ASD.R R/data_iossifov2014ASD.R R/data_itzhak2016.R R/data_itzhak2016markers.R R/data_itzhak2016predictions.R R/data_itzhak2017.R R/data_itzhak2017markers.R R/data_itzhak2017predictions.R R/data_jordan2004psd.R R/data_lee2017shank3proteome.R R/data_lee2017shank3zinc.R R/data_lelieveld2016ID.R R/data_lopitDCmarkers.R R/data_lopitDCpredictions.R R/data_mitocarta2.R R/data_msgene.R R/data_mshallmark.R R/data_neale2012ASD.R R/data_oroak2012ASD.R R/data_orre2019A431.R R/data_orre2019H322.R R/data_orre2019HCC827.R R/data_orre2019MCF7.R R/data_orre2019U251.R R/data_orre2019concensus.R R/data_pdgene.R R/data_peng2004psd.R R/data_phillips2004psd.R R/data_rauch2012ID.R R/data_ripke2014SCHZ.R R/data_sanders2012ASD.R R/data_sanders2015ASD.R R/data_satterstrom2020ASD.R R/data_sfariAnimal.R R/data_sfariGene.R R/data_sharma2015brain.R R/data_spence2019.R R/data_synGO.R R/data_synsysnet.R R/data_takamori2006SV.R R/data_takano2020.R R/data_trinidad2005phosphoPSD.R R/data_trinidad2006phosphoPSD.R R/data_uniprotSubcell.R R/data_uniprot_map.R R/data_urmcDBD.R R/data_velmeshev2019ASD.R R/data_velmeshev2019cells.R R/data_wang2017Epilepsy.R R/data_weingarten2014AZ.R R/data_wilkinson2017gapgef.R R/data_xu2012SZ.R R/documentDataset.R R/e3ligase.R R/geneLists.R R/getHomologs.R R/getIDs.R R/hsKinome.R R/hyperTest.R R/mapIDs.R R/mappingDBs.R R/msKinome.R R/queryMGI.R R/readGMT.R R/uniprotSubcell.R R/writeGMT.R README.md datasets/README.md inst/analysis/0_examples/annotate_corum.R inst/analysis/0_examples/example.R inst/analysis/2_build-lists/.dataset.R inst/analysis/2_build-lists/001_Geisinger-DBD-geneSet.R inst/analysis/2_build-lists/002_Combined-DisGeneNET-DBD-geneSet.R inst/analysis/2_build-lists/003_SFARI-Gene-geneSet.R inst/analysis/2_build-lists/004_SFARI-Animal-geneSet.R inst/analysis/2_build-lists/005_URMC-DBDB-geneSet.R inst/analysis/2_build-lists/006_gene2phenotype-DBD-geneSet.R inst/analysis/2_build-lists/007_Sanders-2015-ASD-geneSet.R inst/analysis/2_build-lists/008_Satterstrom-2020-ASD-geneSet.R inst/analysis/2_build-lists/009_Wang-2017-Epilepsy-geneSet.R inst/analysis/2_build-lists/010_Geladaki-2019-HeLa-LopitDC-Proteome.R inst/analysis/2_build-lists/011_Velmeshev-2019-ASD-geneSet.R inst/analysis/2_build-lists/012_Velmeshev-2019-CellTypes.R inst/analysis/2_build-lists/013_Koopmans-2019-SynGO-geneSet.R inst/analysis/2_build-lists/014_Sharma-2015-Brain-Proteome.R inst/analysis/2_build-lists/015_Uezu-2016-iPSD-Proteome.R inst/analysis/2_build-lists/016_compiled-iPSD-Proteome.R inst/analysis/2_build-lists/017_Wilkinson-2017-GAP-GEF-Proteome.R inst/analysis/2_build-lists/018_Iossifov-2014-ASD-geneSet.R inst/analysis/2_build-lists/019_DeRubeis-2014-ASD-geneSet.R inst/analysis/2_build-lists/020_Fromer-2014-SCHZ-geneSet.R inst/analysis/2_build-lists/021_SynSysNet-Proteome.R inst/analysis/2_build-lists/022_Ripke-2014-SCHZ-geneSet.R inst/analysis/2_build-lists/023_Takamori-2006-SV-Proteome.R inst/analysis/2_build-lists/024_Weingarten-2014-AZ-Proteome.R inst/analysis/2_build-lists/025_Boyken-2013-Presynaptic-Proteome.R inst/analysis/2_build-lists/027_Collins-2006-PSD-Proteome.R inst/analysis/2_build-lists/028_Collins-2005-Synaptic-Phospho-Proteome.R inst/analysis/2_build-lists/029_Jordan-2004-PSD-Proteome.R inst/analysis/2_build-lists/030_Peng-2004-PSD-Proteome.R inst/analysis/2_build-lists/031_Phillips-2004-PSD-Proteome.R inst/analysis/2_build-lists/033_Trinidad-2005-Phospho-PSD-Proteome.R inst/analysis/2_build-lists/034_Dosemeci-2007-PSD95-Proteome.R inst/analysis/2_build-lists/035_Biesemann-2014-Excitatory-Synapse-Proteome.R inst/analysis/2_build-lists/036_Lee-2017-Shank3-Proteome.R inst/analysis/2_build-lists/037_Han-2013-Shank3-Proteome.R inst/analysis/2_build-lists/038_Lelieveld-2016-ID-geneSet.R inst/analysis/2_build-lists/039_Lee-2017-Shank3-Zn-Proteome.R inst/analysis/2_build-lists/040_Chen-2014-AMPAR-Proteome.R inst/analysis/2_build-lists/041_Itzhak-2016-HeLa-Subcellular-Proteome.R inst/analysis/2_build-lists/042_Itzhak-2017-Neuron-Subcellular-Proteome.R inst/analysis/2_build-lists/043_CORUM-Complexes.R inst/analysis/2_build-lists/044_Orre-2019-Subcellular-Proteome.R inst/analysis/2_build-lists/045_MitoCarta2.R inst/analysis/2_build-lists/046_PD-gene.R inst/analysis/2_build-lists/047_Combined-DisGeneNET-NDD-geneSet.R inst/analysis/2_build-lists/048_ALS-gene.R inst/analysis/2_build-lists/049_MS-gene.R inst/analysis/2_build-lists/050_ALZ-gene.R inst/analysis/2_build-lists/051_ALSoD-gene.R inst/analysis/2_build-lists/052_Combined-DisGeneNET-LSD-geneSet.R inst/analysis/2_build-lists/053_HLGD_Lysosome-genes.R inst/analysis/2_build-lists/054_Spence-2019-Wrp-Proteome.R inst/analysis/2_build-lists/055_Dube-2020-Syp-Proteome.R inst/analysis/2_build-lists/056_Gao-IN-PSD95-BioID.R inst/analysis/2_build-lists/057_GSEA-Hallmark-Genes.R inst/analysis/2_build-lists/058_Takano-2020-Tripartite-Synapse-BioID.R inst/analysis/2_build-lists/059_Uezu-2016-ePSD-Proteome.R inst/analysis/2_build-lists/060_Courtland-2020-Brain-Spatial-Proteome.R inst/analysis/2_build-lists/061_UniProt-Subcell-loc.R inst/analysis/2_build-lists/062_Manning2002-Human-Kinome.R inst/analysis/2_build-lists/063_Manning2002-Mouse-Kinome.R inst/analysis/2_build-lists/064_E3-Ligases.R inst/analysis/3_combine-lists/combine-DBD-geneSets.R man/alsgene.Rd man/alsodgene.Rd man/alzgene.Rd man/arrabroadwave3ASD.Rd man/biesemann2014sortedsynaptosomes.Rd man/boyken2013presynapse.Rd man/chen2014AMPARs.Rd man/cheng2006PSD.Rd man/ciPSD.Rd man/collins2005phospho.Rd man/collins2006PSD.Rd man/corum.Rd man/deligt2012ID.Rd man/derubeis2014ASD.Rd man/disgeneDBD.Rd man/disgeneLSD.Rd man/disgeneNDD.Rd man/documentDataset.Rd man/dosemeci2007PSD95proteome.Rd man/e3ligase.Rd man/ePSD.Rd man/fromer2014dbd.Rd man/fromer2014schz.Rd man/g2pDBD.Rd man/geisingerDBD.Rd man/geneLists.Rd man/getHomologs.Rd man/getIDs.Rd man/girard2011SZ.Rd man/gulsuner2013SZ.Rd man/han2013shank3proteome.Rd man/hlgd.Rd man/hsKinome.Rd man/hyperTest.Rd man/iPSD.Rd man/iossifov2012ASD.Rd man/iossifov2014ASD.Rd man/itzhak2016.Rd man/itzhak2016markers.Rd man/itzhak2016predictions.Rd man/itzhak2017.Rd man/itzhak2017markers.Rd man/itzhak2017predictions.Rd man/jordan2004psd.Rd man/lee2017shank3proteome.Rd man/lee2017shank3zinc.Rd man/lelieveld2016ID.Rd man/lopitDCmarkers.Rd man/lopitDCpredictions.Rd man/mapIDs.Rd man/mappingDBs.Rd man/mitocarta2.Rd man/msKinome.Rd man/msgene.Rd man/neale2012ASD.Rd man/oroak2012ASD.Rd man/orre2019A431.Rd man/orre2019H322.Rd man/orre2019HCC827.Rd man/orre2019MCF7.Rd man/orre2019U251.Rd man/orre2019concensus.Rd man/pdgene.Rd man/peng2004psd.Rd man/phillips2004psd.Rd man/queryMGI.Rd man/rauch2012ID.Rd man/read_gmt.Rd man/ripke2014SCHZ.Rd man/sanders2012ASD.Rd man/sanders2015ASD.Rd man/satterstrom2020ASD.Rd man/sfariAnimal.Rd man/sfariGene.Rd man/sharma2015brain.Rd man/spence2019.Rd man/synsysnet.Rd man/takamori2006SV.Rd man/takano2020.Rd man/trinidad2005phosphoPSD.Rd man/trinidad2006phosphoPSD.Rd man/uniprotSubcell.Rd man/urmcDBD.Rd man/velmeshev2019ASD.Rd man/velmeshev2019cells.Rd man/wang2017Epilepsy.Rd man/weingarten2014AZ.Rd man/wilkinson2017gapgef.Rd man/write_gmt.Rd man/xu2012SZ.Rd tests/testthat.R tests/testthat/test-example.R tutorials/064_E3-Ligases.R tutorials/geneLists-usage.R tutorials/getHomologs-usage.R tutorials/getIDs_vs_mapIDs.R tutorials/kang2014-usage.R