NEWS.md

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

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.

neurogenomics/PeakyFinders documentation built on Oct. 14, 2024, 3:09 p.m.