| deepStats aims at providing statistical analyses and streamlining the production of high quality, color-blind friendly, and fully customisable plots (up to the fonts!) for your classic genomic datasets (.bed, .bigwig, gene lists). The goal of deepStats is thus to significantly decrease the amount of time spent in Inkscape/Illustrator to get publication ready plots, and decreasing the research time allotted to finding proper statistical analyses for your genomic signals and datasets.
One of the deepStats tool is dsCompareCurves, which assesses if multiple genomics signals (ChIP-seq, ATAC-seq, etc as .bigwig files) are significantly different or not for multiple region sets (.bed files), and specifically on which bins. dsCompareCurves two methods to do so: bootstraps and per-bin corrected Wilcoxon Rank-sum tests. The input for dsCompareCurves comes from deepTools computeMatrix --outFileNameMatrix, that thus must be used prior to dsCompareCurves. In a nutshell, dsCompareCurves is replacing deepTools plotProfile, but with customisable, scalable and publication ready plots, in addition to providing statistical analyses. dsCompareCurves compares regions for each signal (--comparison regions), or compares all signals for each region set (--comparison scores). Concerning the plots and as the other deepStats tools, a lot of parameters can be customized: plot colors (although the basic color scale is color-blind friendly), fonts, plot size and size ratio. |
hg clone https://toolshed.g2.bx.psu.edu/repos/gtrichard/deepstats_dscomparecurves