deepTools
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deeptools
Tools to process and analyze deep sequencing data.
there might be a duplicate codes in heatmapper.py, method **sort_group** of class _matrix, starting line 1220 to line 1221 ```python elif sort_using == 'mean': matrix_avgs = np.nanmean(matrix, axis=1) elif sort_using...
Dear Professor computeMatrix reference-point --referencePoint TSS -p 15 -b 3000 -a 3000 -R sample.bed -S samole.bw --skipZeros -o sample.gz --outFileSortedRegions sample_genes.bed about sample.bed Is this bed file containing the range...
Hi, I am trying to create a bigwig file using the bamCoverage function for DNAse-seq data and I wanted to check if my implementation is correct. For ATAC-seq I am...
Dear team, I am using the commands below to generate signal profiles over the TSS region and from TSS to TES. However, I have noticed a difference in the Y-axis...
When I am running the following command: `computeMatrix scale-regions --regionsFileName assemblies/mm39/annotation/genes.gtf --scoreFileName $bw --outFileName H3_genebody_ncbiRefSeq_mm39_scaled_noSpikeregions_unscaled.gz --outFileNameMatrix H3_genebody_scaled_noSpikeregions_unscaled.tab --outFileSortedRegions H3_genebody_scaled_noSpikeregions_unscaled.bed --upstream 2000 --downstream 2000 --blackListFileName assemblies/mm39/annotation/blacklist.bed --smartLabels -p 13 --missingDataAsZero --skipZeros`...
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [x] Does the PR contain bugfix?...
The output of plotFingerprint varies depending on the order of BAM files provided in the -b parameter, even when all other arguments remain identical. This affects both the plotted fingerprint...
Dear dev, I think there is no parameter to control for the color of the summary profile in the plotHeatmap. I think would be great to implement this. Best, Lucille
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [ ] Does the PR contain...
Hi deeptools team, thank you for having developed such good tools. The problem I met is that, when combining "computeMatrix scale-regions" and "plotHeatmap", I alwasy see blank regions in the...
