deepTools
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deeptools
Tools to process and analyze deep sequencing data.
The problem in https://stackoverflow.com/questions/72774662/invalid-value-of-type-numpy-float64-received-for-the-y-property-of-scatter also happens in deeptools. I use computeGCBias with --plotFileFormat plotly, it reports the same error.
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If, instead, the protocol is strand-specific, then the first set of integers in a pair would be applied to fragments where read 1 precedes read 2, and the second set...
I am wondering how to sort the sample labels in the legend of `plotCoverage` as natural sort (i.e. `sort -V` in bash or `str_rank(x, numeric = TRUE)` in R) when...
deeptools 3.5.4 Python 3.10.13 Hi! I'm using DeepTools to plot coverage over a list of significantly differential accessible peaks from ATAC-seq data. However, I'm running into a strange issue: the...
Thanks to the great tools provided by the deeptools development team. I have obtained a file with the `computeMatrix reference-point --referencePoint TSS` command, but my TSS result is not very...
Hi, I recently came across this and thought to open an issue for it, I think in line 379, it should be `np.nan` instead of `np.NAN` https://github.com/deeptools/deepTools/blob/master/deeptools/heatmapper.py#L379 For me changing...
Hello, I am new to deepTools and want to run computeMatrix (twice) to study gene promoter effect during activation on 1 mark (H3K4me3) by comparing 2 cell types: 1) activated...
**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [x] Search whether this issue (or a similar issue) has been...
**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [x] Search whether this issue (or a similar issue) has been...