Deeptools

Latest version: v3.5.5

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2.0.1

* A critical bug that prevented plotPCA from running was fixed.
* multiBamCoverage was renamed to multiBamSummary, to be in better alignment with multiBigwigSummary.
* computeGCBias and correctGCBias are now more tolerant of chromosome name mismatches.
* multiBigwigSummary and multiBamSummary can accept a single bigWig/BAM input file, though one should use the
--outRawCounts argument.

2.0.0

* Documentation improved and migrated to http://deeptools.readthedocs.org The API to use deepTools modules is now
part of the documentation and includes a tutorial.
* Allow multiple bigwig files in computeMatrix that can be clustered together
* computeMatrix now accepts multiple bed files. Each bed file is considered as a group. Labels are automatically
added based on the file names.
* When computing read coverage now splited reads are understood. This is convenient for computing the
coverage of for RNA-seq data.
* New quality control tool 'plotCoverage' to plot the coverage over base pairs for multiple samples
* renaming of --missingDataAsZero to --skipNonCovered regions for clarity in bamCoverage and bamCompare
* New analysis tool plotPCA that visualizes the results from principal component analysis
* New option in bamCoverage `--MNase` that will compute the read coverage only considering 2 base pairs at the
center of the fragment.
* Make read extension optional. Remove the need to specify a default fragment length for most of the tools. Now, when
read extension is enabled and the bam files contain paired en data, the mean fragment length is automatically
calculated by sampling the read pairs in the bam file. The --doNotExtendPairedEnds and --fragmentLentgh parameters
are no longer used and the new --extendReads parameter was added.
* Dramatically improved bigwig related tools by using the new pyBigWig module. Eliminated the requirement for the
UCSC program `bigWigInfo`
* renamed heatmapper to plotHeatmap and profiler to plotProfile
* added hierarchical clustering, besides k-means to plotProfile and plotHeatmap
* improved plotting features for plotProfile when using 'overlapped_lines' and 'heatmap' plot types
* Resolved an error introduced by numpy version 1.10 in computeMatrix
* plotting of correlations (from bamCorrelate or bigwigCorrelate) was separated from the computation of the
underlying data. A new tool, plotCorrelation was added. This tool can plot correlations as heatmaps or as scatter
plots and includes options to adjust a large array of visual features.
* Fixed issue with bed intervals in bigwigCorrelate and bamCorrelate and a user specified region.
* Correlation coefficients can be computed even if the data contains NaNs
* Allow computeMatrix to read files with DOS newline characters
* Added option --skipChromosomes to bigwigCorrelate, for example to skip all 'random' chromosomes. bigwigCorrelate
now also considers chromosomes as identical when their names between samples differ with the prefix 'chr'. E.g.
chr1 vs. 1
* For bamCoverage and bamCompare, behaviour of scaleFactor was updated such that now, if given in combination
with the normalization options (normalize to 1x or normalize using RPKM) the given scaleFactor
will multiply the scale factor computed for the normalization methods.
* Fixed problem with read pairs labelled as proper pairs by the aligner but that were actually not proper pairs, for
example because the mates did not face each other. deepTools adds further checks to determine if a read pair is a
proper pair.
* Added titles to QC plots (74)
* Added --samFlagInclude and --samFlagExclude parameters. This is useful to for example only include forward reads
* In deeptools2 most of the core code was rewriting to facilitate API usage and for optimization.

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