NEWS

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MotifPeeker 1.3.3

Miscellaneous

• Add unsupported platform to DESCRIPTION.

MotifPeeker 1.3.2

Bug Fixes

• Bound maximum bootstrapping population size.

Misclaneous

• Update CITATION: MotifPeeker is now published on Bioinformatics Advances!

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 0.99.10

Bug Fixes

• Fix download_button() error when downloadthis package is not available.

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 0.99.6

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.