Files in PriceLab/TrenaProjectErythropoiesis
Temporal Analysis of Erythropoiesis
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/TrenaProjectErythropoiesis.R
README.md
explore/rbp/discordants/ddx3x.vs.discordance.100.genes.R
explore/rbp/discordants/findMotifs.R
explore/rbp/discordants/gene.protein.divergence.categories.RData
explore/rbp/discordants/identifyConDiscordance-rna-srm.R
explore/rbp/discordants/onecut2-repression-obsolete.R
explore/rbp/discordants/scoreRBPs.R
explore/rbp/discordants/survey-rbp-frequencies.R
explore/rbp/discordants/trena-92-ProteinModels-32603x10.RData
explore/rna.protein.discordance/tmt1/runTrenaP.R
explore/rna.protein.discordance/trenaModels/individualGenes/exploreModels.R
explore/rna.protein.discordance/trenaModels/shinyApp/exploreModels.R
explore/rna.protein.discordance/trenaModels/shinyApp/exploreModelsApp.R
explore/rna.protein.discordance/trenaModels/shinyApp/intro.html
explore/rna.protein.discordance/trenaModels/shinyApp/tbl.all.ocCounts.RData
explore/rna.protein.discordance/trenaModels/shinyApp/tbl.trena-100-targets.RData
explore/rna.protein.discordance/trenaModels/shinyApp/tbl.trena-47-targets.RData
explore/rna.protein.discordance/trenaModels/shinyApp/tmsNavigator.R
explore/rna.protein.discordance/trenaModels/shinyApp/toHeatmapMatrix.R
explore/rna.protein.inTimeRegister/brandLabDifferentiationTimeCourse-27171x28-namesCorrected-conformant.RData
explore/rna.protein.inTimeRegister/mtx.itraq-conformant.RData
explore/rna.protein.inTimeRegister/mtx.itraq.RData
explore/rna.protein.inTimeRegister/mtx.srm-conformant.RData
explore/rna.protein.inTimeRegister/mtx.srm.RData
explore/rna.protein.inTimeRegister/mtx.srm.compatible.with.rna.RData
explore/rna.protein.inTimeRegister/prepProteinMatrices.R
explore/rna.protein.inTimeRegister/test_tms-chd1.R
explore/rna.protein.inTimeRegister/tms-chd1.R
explore/slides/ddx3x.pptx
inst/demos/tbx15-represses-gata2/createFimoSqliteDatabase.R
inst/demos/tbx15-represses-gata2/gata2-tbx15-april2019.pdf
inst/demos/tbx15-represses-gata2/tbx15-represses-gata2.R
inst/demos/trenaViz/tv.R
inst/docker/Dockerfile
inst/docker/makefile
inst/docker/packages/makefile
inst/extdata/expression/brandLabDifferentiationTimeCourse-16173x28.RData
inst/extdata/expression/brandLabDifferentiationTimeCourse-27171x28-namesCorrected-conformant.RData
inst/extdata/expression/brandLabDifferentiationTimeCourse-27171x28-namesCorrected.RData
inst/extdata/expression/brandLabDifferentiationTimeCourse-27171x28.RData
inst/extdata/expression/mtx.GSE118537.log+scale.24088x28.RData
inst/extdata/expression/mtx.fpkm.tmt.31760x6.RData
inst/extdata/expression/mtx.itraq-conformant.RData
inst/extdata/expression/mtx.rna.tmt.31761x6.RData
inst/extdata/expression/mtx.srm-conformant.RData
inst/extdata/fimoDBs/fimoResults-2e-4-chr3-128074944-128620958-214k.sqlite
inst/extdata/fimoDBs/gata2.gh.fimoBindingSites.sqlite
inst/extdata/geneSets/basic.txt
inst/extdata/geneSets/srm-103-late-discordance-geneSymbolsAdded.tsv
inst/extdata/genomicRegions/ATAC_brand_d04_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d04_rep2.RData
inst/extdata/genomicRegions/ATAC_brand_d08_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d10_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d10_rep2.RData
inst/extdata/genomicRegions/ATAC_brand_d11_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d11_rep2.RData
inst/extdata/genomicRegions/ATAC_brand_d12_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d12_rep2.RData
inst/extdata/genomicRegions/ATAC_brand_d16_rep1.RData
inst/extdata/genomicRegions/ATAC_brand_d16_rep2.RData
inst/extdata/genomicRegions/ATAC_brand_merged.R
inst/extdata/genomicRegions/prepFiles.R
inst/extdata/genomicRegions/tbl.atacMerged.RData
inst/extdata/harmonized-rna-srm-14-timepoints/merge-rna-srm.R
inst/extdata/harmonized-rna-srm-14-timepoints/mtx-rna-pkfm-27170x14.RData
inst/extdata/harmonized-rna-srm-14-timepoints/mtx-rna-srm-2720x13.RData
inst/extdata/harmonized-rna-srm-14-timepoints/mtx-srm-copyNumber-100x13-someNonStandardNames.RData
inst/extdata/harmonized-rna-srm-14-timepoints/mtx-srm-copyNumber-100x13.RData
inst/extdata/harmonized-rna-srm-14-timepoints/quickLook.R
inst/unitTests/test_TrenaProjectErythro.R
makefile
man/TrenaProjectErythropoiesis-class.Rd
misc/brand-corces-timepoints-compared.pptx
misc/haneyNetwork/haney-pnas-2017-appendix.pdf
misc/haneyNetwork/network.tsv
misc/haneyNetwork/parse.R
misc/multiScore/brandAtacSeqCuration/tbl.atac.fp.RData
misc/multiScore/day0.day2.contrast/earlyActivation.css
misc/multiScore/day0.day2.contrast/earlyActivationApp.R
misc/multiScore/day0.day2.contrast/identifyGenes.R
misc/multiScore/day0.day2.contrast/runTMS.R
misc/multiScore/day0.day2.contrast/simple.R
misc/multiScore/gata2/gata2.R
misc/multiScore/gata2/jaspar2018.meme
misc/multiScore/gata2/tbl.gata2.d12.fp.RData
misc/tenMajorTranscriptionalRegulators/tenMajor.R
misc/tenMajorTranscriptionalRegulators/tmp.meme
prep/bigFimo/combineTrenaModels.R
prep/bigFimo/findProteinsToModelLate.R
prep/bigFimo/generateBigBatch.R
prep/bigFimo/generateBigBindFimoOutput.R
prep/bigFimo/generateBigRunTMS.R
prep/bigFimo/genes-103.R
prep/bigFimo/lookG.R
prep/bigFimo/lookP.R
prep/bigFimo/runBigFimoSingleGene.R
prep/bigFimo/runTMS-old.R
prep/bigFimo/runTMS.R
prep/bigFimo/runTrena.R
prep/bigFimo/runTrenaP.R
prep/compareAtacVsSRM-5timepoints/KLF1.FLI1.atac.srm.RData
prep/compareAtacVsSRM-5timepoints/README.html
prep/compareAtacVsSRM-5timepoints/buildFeatureMatrix.R
prep/compareAtacVsSRM-5timepoints/docker/Dockerfile
prep/compareAtacVsSRM-5timepoints/docker/KLF1.FLI1.atac.srm.RData
prep/compareAtacVsSRM-5timepoints/docker/README.html
prep/compareAtacVsSRM-5timepoints/docker/makefile
prep/compareAtacVsSRM-5timepoints/docker/simpleShinyApp.R
prep/compareAtacVsSRM-5timepoints/findAllBindingSites.R
prep/compareAtacVsSRM-5timepoints/ggplot-explore.R
prep/compareAtacVsSRM-5timepoints/simpleShinyApp.R
prep/compareAtacVsSRM-5timepoints/util.R
prep/docs/TranscriptionalMechanismsUnderlyingHemoglobinSynthesis.pdf
prep/gata-switch/createModels.R
prep/gata-switch/gata2.model.RData
prep/gata-switch/geneRegulatoryModelToGraph.R
prep/gata-switch/tbx15.R
prep/gata-switch/trenaStyle.js
prep/import/srm-from-jeff/SRMforPublication20190614.RData
prep/import/srm-from-jeff/SRMforPublication20190614.txt
prep/import/srm-rna-averaged-final-for-paper/readData.R
prep/import/srm-rna-averaged-final-for-paper/srm.rna.averaged.clean.RData
prep/srm.vs.atac/combineFimoHitsWithSRM.R
viz/srm.vs.mrna/SRMforPublication20190614.RData
viz/srm.vs.mrna/combined/app.R
viz/srm.vs.mrna/combined/linePlot.css
viz/srm.vs.mrna/combined/linePlot.js
viz/srm.vs.mrna/combined/multiPlot.css
viz/srm.vs.mrna/combined/multiPlot.js
viz/srm.vs.mrna/combined/www/app.css
viz/srm.vs.mrna/docker-combined-16aug-2019/Dockerfile
viz/srm.vs.mrna/docker-combined-16aug-2019/app.R
viz/srm.vs.mrna/docker-combined-16aug-2019/combined.R
viz/srm.vs.mrna/docker-combined-16aug-2019/installTrenaCodePrequisites.R
viz/srm.vs.mrna/docker-combined-16aug-2019/linePlot.css
viz/srm.vs.mrna/docker-combined-16aug-2019/linePlot.js
viz/srm.vs.mrna/docker-combined-16aug-2019/makefile
viz/srm.vs.mrna/docker-combined-16aug-2019/multiPlot.css
viz/srm.vs.mrna/docker-combined-16aug-2019/multiPlot.js
viz/srm.vs.mrna/docker-combined-16aug-2019/srm.rna.averaged.clean.RData
viz/srm.vs.mrna/docker-combined-16aug-2019/www/app.css
viz/srm.vs.mrna/docker-combined/Dockerfile
viz/srm.vs.mrna/docker-combined/combined.R
viz/srm.vs.mrna/docker-combined/installTrenaCodePrequisites.R
viz/srm.vs.mrna/docker-combined/linePlot.css
viz/srm.vs.mrna/docker-combined/linePlot.js
viz/srm.vs.mrna/docker-combined/makefile
viz/srm.vs.mrna/docker-combined/multiPlot.css
viz/srm.vs.mrna/docker-combined/multiPlot.js
viz/srm.vs.mrna/docker-combined/srm.rna.averaged.clean.RData
viz/srm.vs.mrna/docker-v6/Dockerfile
viz/srm.vs.mrna/docker-v6/installTrenaCodePrequisites.R
viz/srm.vs.mrna/docker-v6/makefile
viz/srm.vs.mrna/docker-v6/multiPlot.R
viz/srm.vs.mrna/docker-v6/multiPlot.css
viz/srm.vs.mrna/docker-v6/multiPlot.js
viz/srm.vs.mrna/docker-v6/srm.rna.averaged.clean.RData
viz/srm.vs.mrna/docker/Dockerfile
viz/srm.vs.mrna/docker/installTrenaCodePrequisites.R
viz/srm.vs.mrna/docker/linePlot.R
viz/srm.vs.mrna/docker/linePlot.css
viz/srm.vs.mrna/docker/linePlot.js
viz/srm.vs.mrna/docker/makefile
viz/srm.vs.mrna/docker/srm.rna.averaged.clean.RData
viz/srm.vs.mrna/shinyapps.io/app.R
viz/srm.vs.mrna/shinyapps.io/linePlot.css
viz/srm.vs.mrna/shinyapps.io/linePlot.js
viz/srm.vs.mrna/shinyapps.io/multiPlot.css
viz/srm.vs.mrna/shinyapps.io/multiPlot.js
viz/srm.vs.mrna/shinyapps.io/srm.rna.averaged.clean.RData
viz/srm.vs.mrna/shinyapps.io/www/app.css
viz/srm.vs.mrna/srm.vs.mrna.R
viz/srm.vs.mrna/v0/demo-resize.js
viz/srm.vs.mrna/v0/demo.R
viz/srm.vs.mrna/v1/demo-resize.js
viz/srm.vs.mrna/v1/demo.R
viz/srm.vs.mrna/v4/linePlot.R
viz/srm.vs.mrna/v4/linePlot.css
viz/srm.vs.mrna/v4/linePlot.html
viz/srm.vs.mrna/v4/linePlot.js
viz/srm.vs.mrna/v5/multiPlot.R
viz/srm.vs.mrna/v5/multiPlot.css
viz/srm.vs.mrna/v5/multiPlot.js
viz/srm.vs.mrna/v6/multiPlot.R
viz/srm.vs.mrna/v6/multiPlot.css
viz/srm.vs.mrna/v6/multiPlot.js
