GitHub - BaderLab/Brendan_CCInxPred: Can intercellular signals be identified by transcriptional changes?

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docs		docs
.gitignore		.gitignore
200319_compare_datasets.R		200319_compare_datasets.R
200326_lvl3_mixall.R		200326_lvl3_mixall.R
200326_lvl3_umap.R		200326_lvl3_umap.R
200327_lvl3_leaveout1.R		200327_lvl3_leaveout1.R
200327_lvl3_leaveout1_PlateMatched.R		200327_lvl3_leaveout1_PlateMatched.R
200426_lvl5_umap.R		200426_lvl5_umap.R
200427_lvl5_mixall.R		200427_lvl5_mixall.R
200524_lvl5_mixall_leave1out.R		200524_lvl5_mixall_leave1out.R
200615_ctlcorr_inputs.R		200615_ctlcorr_inputs.R
200619_ctldist_inputs.R		200619_ctldist_inputs.R
200621_platematchedLVL3.R		200621_platematchedLVL3.R
200623_lvl4_mixall.R		200623_lvl4_mixall.R
200623_lvl4_mixall_leave1out.R		200623_lvl4_mixall_leave1out.R
200623_lvl4_mixall_metadata.R		200623_lvl4_mixall_metadata.R
200624_DEjaccard.R		200624_DEjaccard.R
200624_DEoverlaptest.R		200624_DEoverlaptest.R
200627_lvl4_umap.R		200627_lvl4_umap.R
200701_lvl5_umap.R		200701_lvl5_umap.R
200703_lvl5_mixall_metadata.R		200703_lvl5_mixall_metadata.R
200706_ZscoreFromAssayed.R		200706_ZscoreFromAssayed.R
200707_lvl4new_mixall.R		200707_lvl4new_mixall.R
200707_lvl4new_mixall_metadata.R		200707_lvl4new_mixall_metadata.R
200708_lvl4_mixall_metadata_pca.R		200708_lvl4_mixall_metadata_pca.R
200708_lvl4_withhold1CT.R		200708_lvl4_withhold1CT.R
200708_lvl5_withhold1CT.R		200708_lvl5_withhold1CT.R
200721_probs_mixall_lvl4.R		200721_probs_mixall_lvl4.R
200730_probs_mixall_breast_lvl3.R		200730_probs_mixall_breast_lvl3.R
200731_probs_mixall_breast_lvl4.R		200731_probs_mixall_breast_lvl4.R
200813_newVall_probs_breast_lvl3.R		200813_newVall_probs_breast_lvl3.R
200813_newVall_probs_breast_lvl4.R		200813_newVall_probs_breast_lvl4.R
200813_newVall_probs_breast_lvl5.R		200813_newVall_probs_breast_lvl5.R
200813_newVall_probs_lvl3.R		200813_newVall_probs_lvl3.R
200813_newVall_probs_lvl4.R		200813_newVall_probs_lvl4.R
200813_newVall_probs_lvl5.R		200813_newVall_probs_lvl5.R
201018_newVall_probs_breast_lvl4_lig16.R		201018_newVall_probs_breast_lvl4_lig16.R
201018_newVall_probs_lvl4_balanced.R		201018_newVall_probs_lvl4_balanced.R
CMapCorr.Rproj		CMapCorr.Rproj
CMapNN_IFNG_fixed.png		CMapNN_IFNG_fixed.png
CMapNN_IFNG_wrong.png		CMapNN_IFNG_wrong.png
CMapNN_TNF_fixed.png		CMapNN_TNF_fixed.png
CMapNN_TNF_wrong.png		CMapNN_TNF_wrong.png
CellStimPred_lvl3.Rmd		CellStimPred_lvl3.Rmd
CmapCtrlCorr.Rmd		CmapCtrlCorr.Rmd
CmapDataSummary.Rmd		CmapDataSummary.Rmd
CmapNN_outputfigs.R		CmapNN_outputfigs.R
DEbackground.R		DEbackground.R
DEoverlap.Rmd		DEoverlap.Rmd
DEoverlap_FDR.Rmd		DEoverlap_FDR.Rmd
DEoverlap_FDR_forPaper.Rmd		DEoverlap_FDR_forPaper.Rmd
DEoverlap_NicheNet.R		DEoverlap_NicheNet.R
DEoverlap_NicheNet_earlygarbage.R		DEoverlap_NicheNet_earlygarbage.R
Fig4.Rmd		Fig4.Rmd
Fig_corr.R		Fig_corr.R
Fig_corr_compareall.png		Fig_corr_compareall.png
Fig_corr_compareallperligand.png		Fig_corr_compareallperligand.png
Fig_corr_ct.png		Fig_corr_ct.png
Fig_corr_lig.png		Fig_corr_lig.png
Fig_corr_ligct.png		Fig_corr_ligct.png
Fig_corr_rep.png		Fig_corr_rep.png
GEOlabs.R		GEOlabs.R
GEOlabs.txt		GEOlabs.txt
GSEA.R		GSEA.R
GSEA_PhitsSCORE.R		GSEA_PhitsSCORE.R
GSEA_PmeanFDRscore.R		GSEA_PmeanFDRscore.R
GSEA_PmeanFDRscore_downsampled.R		GSEA_PmeanFDRscore_downsampled.R
GSEA_PmeanFDRscore_downsampled_v2.R		GSEA_PmeanFDRscore_downsampled_v2.R
GSEA_PmeanNES.R		GSEA_PmeanNES.R
GSEA_PmeanNES2.R		GSEA_PmeanNES2.R
GSEA_meanES.R		GSEA_meanES.R
GSEA_meanES_testing.R		GSEA_meanES_testing.R
GSEA_meanZ.R		GSEA_meanZ.R
GSEA_overlapLVL5.R		GSEA_overlapLVL5.R
GSEA_v2.R		GSEA_v2.R
GSEAcorr.R		GSEAcorr.R
GSEAcorr.Rmd		GSEAcorr.Rmd
GSEAcorr2.Rmd		GSEAcorr2.Rmd
GSEAcorr_v2.R		GSEAcorr_v2.R
LINCS2020 Release Metadata Field Definitions.xlsx		LINCS2020 Release Metadata Field Definitions.xlsx
LigPred_extrapolate.Rmd		LigPred_extrapolate.Rmd
LigPred_lvl4.Rmd		LigPred_lvl4.Rmd
LigPred_lvl5.Rmd		LigPred_lvl5.Rmd
LigProb_NovelLines.Rmd		LigProb_NovelLines.Rmd
LigProb_lvl3_breast.Rmd		LigProb_lvl3_breast.Rmd
LigProb_lvl4.Rmd		LigProb_lvl4.Rmd
NNdatacheckup.R		NNdatacheckup.R
NicheNet.Rmd		NicheNet.Rmd
NicheNetFig1data.xlsx		NicheNetFig1data.xlsx
NicheNetSuppTable3.xlsx		NicheNetSuppTable3.xlsx
NicheNet_ALLvCT_DEovlp_matrix.R		NicheNet_ALLvCT_DEovlp_matrix.R
NicheNet_DBinfo.txt		NicheNet_DBinfo.txt
NicheNet_DBinfo_nDE.txt		NicheNet_DBinfo_nDE.txt
NicheNet_LigDEoverlap_count.txt		NicheNet_LigDEoverlap_count.txt
NicheNet_LigDEoverlap_ratio.txt		NicheNet_LigDEoverlap_ratio.txt
NicheNet_calc.R		NicheNet_calc.R
NicheNet_calc_ALLvCT.R		NicheNet_calc_ALLvCT.R
NicheNet_calc_noTS.R		NicheNet_calc_noTS.R
NicheNet_data_sources.xlsx		NicheNet_data_sources.xlsx
NicheNet_forPaper.Rmd		NicheNet_forPaper.Rmd

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Can intercellular signals be identified by transcriptional changes?

baderlab.github.io/Brendan_CCInxPred/

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