MIRs-IDH12-DNMT3A-AMLs_2022

Step00* | Find TADs, make expression and methylation datasets

Step01* | Expression and methylation differences

Step02* | Correlations within TADs

Step03* | Architecture

Step04* | Histone marks and TFs

Step05* | TCGA analyses

Step06* | Methylation of repeat elements

Step07* | Mouse expression data

Step08* | Normal hematopoiesis

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
Functions.py		Functions.py
README.md		README.md
Step000.TADs.sh		Step000.TADs.sh
Step001.MakeMethylData.py		Step001.MakeMethylData.py
Step002.MakeExprData.r		Step002.MakeExprData.r
Step003.Combine.py		Step003.Combine.py
Step004.ExprWtWt.r		Step004.ExprWtWt.r
Step005.MakeWtWtDataset.py		Step005.MakeWtWtDataset.py
Step011.ExprDifferences.r		Step011.ExprDifferences.r
Step012.MethylDifferences.r		Step012.MethylDifferences.r
Step013.GSEA.sh		Step013.GSEA.sh
Step014.AnnotateTSS.py		Step014.AnnotateTSS.py
Step021.PrepareTADs.sh		Step021.PrepareTADs.sh
Step022.MakePairs.py		Step022.MakePairs.py
Step023.Correlations.py		Step023.Correlations.py
Step024.ProcessCorrs.r		Step024.ProcessCorrs.r
Step025.TadChars.py		Step025.TadChars.py
Step026.r		Step026.r
Step027.Same_Ranks_Lipids.py		Step027.Same_Ranks_Lipids.py
Step028.GseaDavid.sh		Step028.GseaDavid.sh
Step029.PlotPaths.r		Step029.PlotPaths.r
Step02A.DeDmCorrs_Pairs.r		Step02A.DeDmCorrs_Pairs.r
Step02B.HoxSnx.r		Step02B.HoxSnx.r
Step02C.MakeKeggNets.py		Step02C.MakeKeggNets.py
Step02D.CpGislands.py		Step02D.CpGislands.py
Step02E.r		Step02E.r
Step02F.Rank.py		Step02F.Rank.py
Step02G.GSEA.sh		Step02G.GSEA.sh
Step02H.CompareMcCpg.py		Step02H.CompareMcCpg.py
Step02I.r		Step02I.r
Step02J.CorrWtWt.py		Step02J.CorrWtWt.py
Step02K.r		Step02K.r
Step031.Prepare1.sh		Step031.Prepare1.sh
Step032.Prepare2.py		Step032.Prepare2.py
Step033.Prepare3.py		Step033.Prepare3.py
Step034.CheckArchitecture.py		Step034.CheckArchitecture.py
Step035.mCs.py		Step035.mCs.py
Step036.Plot_mCs.r		Step036.Plot_mCs.r
Step037.Plot_Genes.r		Step037.Plot_Genes.r
Step038.SpecificMIRs.py		Step038.SpecificMIRs.py
Step039.BBoxInsulHist.sh		Step039.BBoxInsulHist.sh
Step03A.BBoxEvol.py		Step03A.BBoxEvol.py
Step03B.r		Step03B.r
Step03C.prepGC.py		Step03C.prepGC.py
Step03D.MIRcontent.r		Step03D.MIRcontent.r
Step041.MonteCarlo.sh		Step041.MonteCarlo.sh
Step042.ProcessSims.py		Step042.ProcessSims.py
Step043.Plot_TFsGenes.r		Step043.Plot_TFsGenes.r
Step044.Plot_TFsCs.r		Step044.Plot_TFsCs.r
Step045.PPIs.py		Step045.PPIs.py
Step046.r		Step046.r
Step051.GetPairs.sh		Step051.GetPairs.sh
Step052.Pairs_Datasets.py		Step052.Pairs_Datasets.py
Step053.Correlate.py		Step053.Correlate.py
Step054.r		Step054.r
Step055.Rank.py		Step055.Rank.py
Step056.GseaDavid.sh		Step056.GseaDavid.sh
Step057.PlotPaths.r		Step057.PlotPaths.r
Step058.Archit_GenesCs.py		Step058.Archit_GenesCs.py
Step059.Misc.r		Step059.Misc.r
Step05A.CompareGlassTCGA.py		Step05A.CompareGlassTCGA.py
Step05B.r		Step05B.r
Step05C.NonMutants.py		Step05C.NonMutants.py
Step05D.Correlate.py		Step05D.Correlate.py
Step05E.r		Step05E.r
Step061.Methylation_Reps.r		Step061.Methylation_Reps.r
Step062.GEAR.py		Step062.GEAR.py
Step063.Enhancers.sh		Step063.Enhancers.sh
Step064.Plots.r		Step064.Plots.r
Step071.SraFiles.sh		Step071.SraFiles.sh
Step072.MakeDataset.py		Step072.MakeDataset.py
Step073.r		Step073.r
Step074.David.sh		Step074.David.sh
Step075.Arch.py		Step075.Arch.py
Step076.Plot.r		Step076.Plot.r
Step081.IDs.py		Step081.IDs.py
Step082.ProcessAffy.r		Step082.ProcessAffy.r
Step083.Architecture.py		Step083.Architecture.py
Step084.r		Step084.r
Step085.Projections.r		Step085.Projections.r

atelonis/MIRs-IDH12-DNMT3A-AMLs_2022

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