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Changelog

Source: NEWS.md

MotifPeeker 1.3.1

Section Rework

  • Motif-summit distances
    • Remove distances by peak count.
    • Reword descriptions
    • [NEW] Add bootstrapping to visualise the distribution of motif-summit distances.

New Features

  • Add support for directly importing “mm10” and “mm39” mouse genome builds.
  • read_motif_file can now accept an universalmotif object, returns the same object.
  • Input datasets section now reports datasets in a tabular form.

Documentation

  • Improve instructions for importing genome builds.
  • Improve instructions for importing motifs.

MotifPeeker 1.1.3

Miscellaneous

  • Changed import to use Seqinfo instead of GenomeInfoDb.

MotifPeeker 1.1.2

Miscellaneous

  • Only consider unique peaks in peak count.
  • Only return unique peaks in segregate_seqs().

Bug Fixes

  • Sanitise peak input names before running FIMO.

MotifPeeker 1.1.1

Bug Fixes

  • Fix importing MACS peak files with no peak names.
  • Update tests for messager().

Miscellaneous

  • Add citation to pre-print.
  • Switch to the official repo for rworkflows.

MotifPeeker 0.99.13

Bug Fixes

  • Fix missing second table in known motif enrichment analysis tabs.

Miscellaneous

  • Add “in Bioc” badge to README.

MotifPeeker 0.99.12

Bug Fixes

  • Supply meme_path and verbose to second motif_enrichment call in get_df_enrichment.

Miscellaneous

  • Update example reports.
  • Add new author.
  • Add BioConductor installation instructions to README.

MotifPeeker 0.99.11

Miscellaneous

  • Correct “de-novo motif discovery” term to “motif discovery”. STREME does not perform de-novo motif discovery.
  • Add package version to report header.

MotifPeeker 0.99.9 / 0.99.10

Bug Fixes

MotifPeeker 0.99.8

Miscellaneous

  • Optimise examples and remove \donttest{} blocks.
  • Add GitHub Actions for rworkflows without MEME Suite.

MotifPeeker 0.99.7

New Features

  • Replace workers argument with BPPARAM. Give users more control over the BiocParallel implementation.

Miscellaneous

  • Remove cat() calls in functions.
  • Implement helper check_input() to validate input before passing them to other functions.
  • Run examples and tests only if MEME Suite is detected (only for functions which require MEME Suite).

MotifPeeker 0.99.5 / 0.99.6

Miscellaneous

  • Replace magrittr import by dplyr::%>%.
  • Reduce the number of exported functions.
  • Move utility functions to ‘utilities.R’.
  • Allow vignettes to run without MEME suite installed.
  • Remove stopper() wrapper around stop().
  • Use message() for parallel executions

MotifPeeker 0.99.4

Miscellaneous

  • Switch to a smaller file to download in check_ENCODE example.
  • Move some code outside \donttest{} to prevent BiocCheck() error about missing examples.

MotifPeeker 0.99.3

Miscellaneous

  • Wrap certain examples under \donttest{} to reduce R CMD CHECK runtime.
  • [GitHub] Add CODECOV_TOKEN secret to rworkflows.
  • Skip running tests which require download if offline.

MotifPeeker 0.99.2

Miscellaneous

  • Substitute system() with system2().
  • Reduce denovo_motifs in examples and tests to reduce R CMD CHECK runtime.
  • Add .BBSoptions to .Rbuildignore.

MotifPeeker 0.99.1

Miscellaneous

  • .BBSoptions added to skip Windows builders on Bioconductor.

MotifPeeker 0.99.0

New features

  • MotifPeeker submitted to Bioconductor.