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multiBigwigSummary multiBigwigSummary -b file1.bw file2.bw -out results.npz --BED selection.bed This tool computes the average scores for every genomic region for every bigWig file that is provided. In principle, it does the same as multiBamSummary, but for bigWig files. The analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions (e.g., genes) in 'BED-file' mode. Typically the output of multiBigwigSummary is used by other tools, such as plotCorrelation or plotPCA, for visualization and diagnostic purposes. Show
plotProfile plotProfile [--outFileSortedRegions FILE] This tool creates a profile plot for scores over sets of genomic regions. Typically, these regions are genes, but any other regions defined in BED will work. A matrix generated by computeMatrix is required. Show
plotProfile plotProfile [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] This tool creates a profile plot for scores over sets of genomic regions. Typically, these regions are genes, but any other regions defined in BED will work. A matrix generated by computeMatrix is required. Show
plotEnrichment plotEnrichment [FILE1.bed FILE2.bed ...] --plotFile FILE This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotProfile plotProfile [--matrixFile MATRIXFILE] --outFileName OUTFILENAME This tool creates a profile plot for scores over sets of genomic regions. Typically, these regions are genes, but any other regions defined in BED will work. A matrix generated by computeMatrix is required. Show
plotEnrichment plotEnrichment[file1.bam file2.bam ...] --BED FILE1.bed FILE2.bed This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--labels sample1 sample2 [sample1 sample2 ...]] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--region CHR:START:END] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--numberOfProcessors INT] [--verbose] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--minMappingQuality INT] [--centerReads] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [-h] --bamfiles file1.bam file2.bam This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--Offset INT [INT ...]] [--keepExons] [--version] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--samFlagInclude INT] [--samFlagExclude INT] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--outRawCounts FILE] [--perSample] [--variableScales] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotCorrelation plotCorrelation [-h] --corData FILE --plotFile FILE --corMethod {spearman,pearson} --whatToPlot {heatmap,scatterplot} This tools takes the default output of multiBamSummary or multiBigwigSummary, and computes the pairwise correlation among samples. Results can be visualized as scatterplots or as a heatmap of correlation coefficients Show
plotEnrichment plotEnrichment [--regionLabels region1 region2 [region1 region2 ...]] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--blackListFileName BED file [BED file ...]] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--numPlotsPerRow NUMPLOTSPERROW] [--alpha ALPHA] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show
plotEnrichment plotEnrichment [--colors COLORS [COLORS ...]] This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed. Show