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deepTools 2.0
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@fidelram fidelram released this 21 Jan 14:07
· 1948 commits to master since this release
2.0.0
2883409

Major changes

  • computeMatrix now accepts multiple bigwig files that can later be plotted together as heatmaps
    one after the other or as multiple lines in the same plot. See the documentation of plotHeatmap
    and plotProfile for examples.
  • computeMatrix also now accepts multiple input BED files. Each is treated as a group within a sample
    and is plotted independently.
  • Added new analysis tool :doc:tools/plotPCA to visualize the results of multiBamCoverage
    or tools/multiBigwigSummary using principal component analysis.
  • Added new quality control tool tools/plotCoverage to plot the coverage over base pairs for multiple samples
  • Dramatically improved the speed of bigwig related tools (multiBigwigSummary and computeMatrix)
    by using the new pyBigWig module.
  • Added support for split reads (most commonly found in RNA-seq data).
  • Added new option --MNase in bamCoverage that computes reads coverage only considering two
    base pairs at the center of the fragment.
  • Added --samFlagInclude and --samFlagExclude parameters. This is useful to for example
    only include forward reads (or only reverse reads) in an analysis.
  • Plotting of correlations (from multiBamCoverage or multiBigwigSummary) is now
    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.
  • Added hierarchical clustering, besides k-means to plotProfile and plotHeatmap
  • Correlation coefficients can now be computed even if the data contains NaNs.
  • The documentation was migrated to http://deeptools.readthedocs.org
  • deepTools modules can now be used by other python programs. The :ref:api is now part of the documentation.
  • In this new release, most of the core code was rewriting to facilitate API usage and for optimization.

Minor changes

  • --missingDataAsZero was renamed to --skipNonCoveredRegions for clarity in :doc:tools/bamCoverage
    and :doc:tools/bamCompare.
  • Read extension was made optional and removed the need to specify a default fragment length for most of the tools.
    and --fragmentLentgh parameters were replaced by the new optional parameter --extendReads.
  • Renamed:
    • heatmapper to :doc:tools/plotHeatmap
    • profiler to :doc:tools/plotProfile
    • bamCorrelate to multiBamCoverage
    • bigwigCorrelate to multiBigwigSummary
    • bamFingerprint to :plotFingerprint.
  • Improved plotting features for plotProfile when using as plot type: 'overlapped_lines' and 'heatmap'
  • Resolved an error introduced by numpy version 1.10 in :doc:tools/computeMatrix
  • Fixed problem with bed intervals in multiBigwigSummary and multiBamCoverage and a
    user specified region that returned wrongly labeled raw counts.
  • computeMatrix can now read files with DOS newline characters.
  • Added option --skipChromosomes to :doc:tools/multiBigwigSummary, for example to skip all
    'random' chromosomes. multiBigwigSummary now also considers chromosomes as identical
    when the names between samples differ by 'chr' prefix 'chr'. E.g. chr1 vs. 1
  • For :doc:tools/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 wrongly labeled proper pairs in a bam file. deepTools adds further checks to
    determine if a read pair is a proper pair.
  • Added titles to QC plots,
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