Files in robinweide/GENOVA
GENOVA: expore the Hi-C

.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
GENOVA.Rproj
LICENSE
LOGO.jpg
LOGO.pdf
Manuscript/setup.txt
NAMESPACE
R/.DS_Store
R/APA.R R/ATA.R R/HiC_matrixplot.R R/PESCAn.R R/RCP2.R
R/RCP_OLD.txt
R/antoni.Rdat
R/badBin.find.R R/badBin.plot.R R/centromere_telomere.R R/chromosomeMatrix.R R/cisTotal.perChrom.R R/cisTotal.scores.R R/compartment.score.R R/construct.experiment.R R/cov2d.R R/differential.TAD.dotplot.R R/differential.TAD.scatterplot.R R/eigen_plot.R R/fastDI.R R/fields.interp.surface.R R/frequency.from.matrix.R R/insulation.callTAD.R R/insulation.heatmap.R R/insulation_score.R R/intra.inter.TAD.contacts.R
R/notes/findCorners
R/notes/fullToHicPro
R/notes/iso_tad_calling
R/notes/painting.R
R/notes/saddle_old
R/notes/transLocMasker.R
R/notes/transLocMasker.R.rtf
R/plot.chrom.comparison.R R/quantifyAPA.R R/read.bedpe.R R/read.hicpro.matrix.R R/rescale.R R/resize.mat.R R/saddleFunctions.R R/select.sub.2D.R R/select.sub.R R/select.subset.R R/shuffleHiC.R R/virtual.4C.R R/visualise.APA.base.R R/visualise.APA.ggplot.R R/visualise.ATA.ggplot.R R/visualise.RCP.ggplot.R R/visualise.virtual.4C.R README.md fig1.pdf lookupTIme.R lookupTIme.pdf man/APA.Rd man/ATA.Rd man/PESCAn.Rd man/PESCAn_covert.Rd man/RCP.Rd man/badBin.find.Rd man/badBin.plot.Rd man/centromere.telomere.analysis.Rd man/chrom.comparison.plot.Rd man/chromosome.wide.insulation.Rd man/chromosomeMatrix.Rd man/cis.compartment.plot.Rd man/cisTotal.perChrom.Rd man/cisTotal.scores.Rd man/compartment.score.Rd man/construct.experiment.Rd man/cov2d.Rd man/differential.TAD.dotplot.Rd man/differential.TAD.scatterplot.Rd man/draw.centromere.telomere.Rd man/fastDI.Rd man/fields.interp.surface.Rd man/frequency.from.matrix.Rd man/genome.wide.insulation.Rd man/hic.matrixplot.Rd man/insulation.callTAD.Rd man/insulation.domainogram.Rd man/insulation.heatmap.Rd man/insulation.plot.dual.Rd man/insulation.plot.single.Rd man/insulation.polygon.Rd man/insulation.score.Rd man/intra.inter.TAD.contacts.Rd man/matrix.insulation.Rd man/quantifyAPA.Rd man/read.bedpe.Rd man/read.hicpro.matrix.Rd man/rescale.Rd man/resize.mat.Rd man/saddle.Rd man/select.sub.2D.Rd man/select.sub.Rd man/select.subset.Rd man/shuffleHiC.Rd man/trans.compartment.plot.Rd man/virtual.4C.Rd man/visualise.APA.base.Rd man/visualise.APA.ggplot.Rd man/visualise.ATA.ggplot.Rd man/visualise.PESCAn.ggplot.Rd man/visualise.RCP.ggplot.Rd man/visualise.compartmentStrength.Rd man/visualise.saddle.Rd man/visualise.virtual.4C.Rd
scripts/juicerToGenova.py
t1logo.jpg
vignettes/.DS_Store
vignettes/GENOVA.bib
vignettes/GENOVA_vignette.R vignettes/GENOVA_vignette.Rmd vignettes/GENOVA_vignette.pdf
vignettes/GENOVA_vignette_cache/latex/__packages
vignettes/GENOVA_vignette_files/figure-latex/APAplot-1.pdf
vignettes/GENOVA_vignette_files/figure-latex/ATAplot-1.png
vignettes/GENOVA_vignette_files/figure-latex/CCP1-1.png
vignettes/GENOVA_vignette_files/figure-latex/CCP1-2.png
vignettes/GENOVA_vignette_files/figure-latex/CCP3-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMP1-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPall-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPchip-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPchipGene-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPdiff1-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPdiff1-2.png
vignettes/GENOVA_vignette_files/figure-latex/HMPtadloop-1.png
vignettes/GENOVA_vignette_files/figure-latex/HMPtadloop-2.png
vignettes/GENOVA_vignette_files/figure-latex/INSalign-1.png
vignettes/GENOVA_vignette_files/figure-latex/PESCAn-1.pdf vignettes/GENOVA_vignette_files/figure-latex/RCPBED-1.pdf vignettes/GENOVA_vignette_files/figure-latex/RCPPLOT1-1.pdf vignettes/GENOVA_vignette_files/figure-latex/RCPPLOT2-1.pdf
vignettes/GENOVA_vignette_files/figure-latex/TCP-1.png
vignettes/GENOVA_vignette_files/figure-latex/cent2-1.pdf vignettes/GENOVA_vignette_files/figure-latex/chromMat1-1.pdf vignettes/GENOVA_vignette_files/figure-latex/cis-1.pdf vignettes/GENOVA_vignette_files/figure-latex/cis2-1.pdf
vignettes/GENOVA_vignette_files/figure-latex/domainogram-1.png
vignettes/GENOVA_vignette_files/figure-latex/domainogram2-1.png
vignettes/GENOVA_vignette_files/figure-latex/iiDIFF-1.png
vignettes/GENOVA_vignette_files/figure-latex/iiDIFF2-1.png
vignettes/GENOVA_vignette_files/figure-latex/pePERS-1.pdf
vignettes/GENOVA_vignette_files/figure-latex/plotTADCALLS-1.png
vignettes/GENOVA_vignette_files/figure-latex/quantAPA-1.pdf vignettes/GENOVA_vignette_files/figure-latex/saddlePlot-1.pdf vignettes/GENOVA_vignette_files/figure-latex/saddleStrength-1.pdf vignettes/GENOVA_vignette_files/figure-latex/saddleStrength-2.pdf vignettes/chr1.pdf
vignettes/data/CTCF_WT.bw
vignettes/data/CTCF_WT_motifs.bed
vignettes/data/GSE74072_Hap1_HiCCUPS_looplist.txt.gz
vignettes/data/H3K27ac_WT.narrowPeak
vignettes/data/SCC4_10kb_abs.bed
vignettes/data/SCC4_10kb_iced.matrix
vignettes/data/SMC1_WAPL.bw
vignettes/data/SMC1_WT.bw
vignettes/data/SMC1_WT_peaks.narrowPeak
vignettes/data/WAPL_1000000_abs.bed
vignettes/data/WAPL_1000000_iced.matrix
vignettes/data/WAPL_10000_abs.bed
vignettes/data/WAPL_10000_iced.matrix
vignettes/data/WAPL_40000_abs.bed
vignettes/data/WAPL_40000_iced.matrix
vignettes/data/WT_1000000_abs.bed
vignettes/data/WT_1000000_iced.matrix
vignettes/data/WT_10000_abs.bed
vignettes/data/WT_10000_iced.matrix
vignettes/data/WT_3Mb_extended_loops.bed
vignettes/data/WT_40000_abs.bed
vignettes/data/WT_40000_iced.matrix
vignettes/data/WT_HICCUPS.bedpe
vignettes/data/WT_hicseg_TADs.bed
vignettes/data/c01ff14317d7a70d303a7bf37ef29ab4.jpg
vignettes/data/hg19_cytobandAcen.bed
vignettes/data/homerSuperEnhancers.txt
vignettes/data/mart_export.txt.gz
vignettes/data/nintchdbpict000277131838.jpg?w=811
vignettes/data/refGene_hg19.tsv.gz
robinweide/GENOVA documentation built on May 26, 2018, 7:05 a.m.