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PeakyFinders 0.99.4

New features

  • Implement rworkflows.

PeakyFinders 0.99.3

New features

  • import_peaks:
    • Can now recognize and read in local/remote file paths passed to ids.
    • New subfunction import_peaks_files to support this.
  • create_trackhub:
    • New set of functions to automatically creating UCSC Genome Browser TrackHubs from bigwig, bedGraph, bed, bedGraph files.
  • New function: bed_to

Bug fixes

  • Make min R version 4.1.

PeakyFinders 0.99.2

New features

  • call_peaks:
    • SEACR now implemented!!
    • Add parameters as metadata in peak GRanges.
  • New exported functions:
    • merge_bam: Merge multiple BAM files into one.
    • pooled_peaks: Pool groups of BAM files and call peaks from them (using either MACSr or SEACR).
    • convert_bam: Convert BAM file to any format.
    • example_bg_bw
    • example_bam
  • New internal functions:
    • report_time
    • import_peaks_seacr
    • import_peaks_macs
    • call_peaks_seacr
    • pooled_peaks_seacr/ pooled_peaks_macsr
    • make_conda_env
    • find_executable_seacr
    • add_mcol
    • bam_to
  • Change all call_peaks_method args to simpler --> method.

Bug fixes

  • import_peaks_*: Now handle situations where 0 peaks are called.
  • import_peaks: Add support to bigBed format.
  • Switch from BiocParallel to parallel, as the former is extremely buggy and inconsistent.

PeakyFinders 0.99.1

New features

  • Add generic find_links function.

Bug fixes

  • Removed duplicated files from Google Drive ("(1).R").
  • Accidentally hard-coded a GSM ID into process_ids.
  • Extract supp files from both the project-level GSE ID and sample-level GSM ids.
  • Figure out why package is unable to find "peaks_metadata_roadmap" unless package is loaded.
  • Force all rownames to be unique.

PeakyFinders 0.99.0

Bug fixes

  • Select SnowParam vs. SerialParam depending on OS to avoid issues on Windows.
  • Fix vignette formatting.
  • Add error handlers for import.bw on Windows (until someone fixes rtracklayer).
  • Add error handlers for MACSr on Windows (until it becomes compatible).
  • Remove import_bigwig_filtered function (not used).

New features

  • Added a NEWS.md file to track changes to the package.
  • Set GHA to push to DockerHub.
  • Give call_peaks_macsr it's own subfunction.
  • Add conda env.