Bioinformatic analysis of RNA-Seq, WGBS, and Hi-C in Arabidopsis thaliana
Date: 2019-12-26
|-- Hi-C_Processing
| |-- BatchCompareHi-C_100K.sh
| |-- BatchPlotPGT.sh
| |-- CompareHeatAndControl_CompartmentStrength_SaddlePlot.R
| |-- CompareHi-C_WithPreviousPublishedHi-C_ByFPC.R
| |-- ComparePC1BedGraph_WithABCompartmentChangeInfo.R
| |-- CompareTwoHiCmatrixV2BasedOnHiCdat.R
| |-- CrossCompare_Two_Hi-C_Rep12.R
| |-- Heat-activated_TEs_PlusPC1Info.R
| |-- HiC_Heatmap_Generator.R
| |-- Hi-C_ScalingPlotGeneratorFromHiC-ProUsingHiCE_001kb.sh
| |-- Hi-C_ScalingPlotGeneratorFromHiC-ProUsingHiCE_100kb.sh
| |-- KEExKEEyInteractionsPersp3D.R
| |-- NoScaleHiCPlotDistVsCounts.py
| |-- PlotDistVsCounts.R
| |-- PlotLocalRescaled2DMetaChromatinOrganizationOverHeatActivatedTEs.R
| |-- RepHIC.ini
| |-- TEKEE34_MinMax.ini
| |-- theme_linhua.R
| `-- UpdatedPlotDistVsCounts.R
|-- NotUsed.tgz
|-- Others
| |-- HeatStressNuclearSizeDistributionCompare.R
| `-- PlotKEEsDistancesDistributionMBPVersion20191028.R
|-- README.md
|-- RNA-Seq_Processing
| |-- 01_Heat_polyA-RNA-Seq_DifferentialAnalysis_PlusExpressionInfo_2019.R
| |-- 02_Heat_polyA-RNA-Seq_PCG_Scatterplot.R
| |-- 03_Heat_polyA-RNA-Seq_TE_Chromosome-wide-Plot.R
| |-- 04_Heat_polyA-RNA-Seq_TE_Expression_Dynamics_Analysis.R
| |-- 05_Heat_polyA-RNA-Seq_TE_Combine_Expression_Distribution.R
| |-- 4VS4_RNA-seq-polyA-FeatureCounts-Batch-DEG-Analysis-TE-Version.R
| |-- EpiFeaturesEnrcihmentAnalaysisHeatmap.R
| |-- Heat_Activated_TEs_Detailed_Analysis-Enrichment.R
| |-- Heat_Activated_TEs_MainEnrichment.R
| |-- SingleGroupTEBasicFeaturesEnrichmentAnalysis_20191119.R
| `-- ss_SE_US_RNA-Seq_Ath.sh
`-- WGBS_Processing
`-- PE_WGBS_MethylPy.sh