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extrachips

https://github.com/smped/extrachips

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene ontology sequencing genomics immune-repertoire proteomics grna-sequence multiview heatmap
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Created almost 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

extraChIPs

Build Status Codecov test coverage Repo Status <!-- badges: end -->

extraChIPs is a package primarily designed to enable ChIP-Seq analysis. Whilst the package was primarily built for the GRAVI: Gene Regulatory Analysis using Variable Inputs
workflow, the functionality extends beyond this specific application. Functions focus primarily on

  • Retaining mcols() when manipulating GRanges objects
  • Common visualisation utilities for ChIP-Seq analysis
  • Enabling sliding window analysis for differential ChIP-target binding

It is intended that these functions will integrate seamlessly with other packages such as those provided in csaw, plyranges and limma.

In addition to enabling workflows, simple coercion to tibble objects from DataFrame, GRanges and GInteractions objects is implemented.

Installation Instructions

To install this package from Bioconductor, please use BiocManager.

r install.packages("BiocManager") BiocManager::install("extraChIPs")

To install the development version from github

r BiocManager::install("smped/extraChIPs")

Owner

  • Name: Stevie Pederson
  • Login: smped
  • Kind: user
  • Location: Adelaide, Australia
  • Company: Black Ochre Data Labs, Telethon Kids Institute

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 32
  • Create event: 2
Last Year
  • Issues event: 2
  • Issue comment event: 1
  • Push event: 32
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 357
  • Total Committers: 7
  • Avg Commits per committer: 51.0
  • Development Distribution Score (DDS): 0.081
Past Year
  • Commits: 141
  • Committers: 4
  • Avg Commits per committer: 35.25
  • Development Distribution Score (DDS): 0.043
Top Committers
Name Email Commits
Steve Pederson s****u@g****m 328
Steve Ped s****n@a****u 13
Steve Pederson s****d 8
J Wokaty j****y@s****u 2
Nitesh Turaga n****a@g****m 2
Stevie Pederson 8****d 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 adelaide.edu.au: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 12
  • Total pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • smped (10)
  • tamerbio (2)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • BiocParallel * depends
  • GenomicRanges * depends
  • R >= 4.2.0 depends
  • SummarizedExperiment * depends
  • ggplot2 * depends
  • tibble * depends
  • BiocIO * imports
  • ComplexUpset * imports
  • EnrichedHeatmap * imports
  • GenomeInfoDb * imports
  • GenomicInteractions * imports
  • Gviz * imports
  • IRanges * imports
  • InteractionSet * imports
  • RColorBrewer * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • VennDiagram * imports
  • broom * imports
  • csaw * imports
  • dplyr * imports
  • edgeR * imports
  • forcats * imports
  • ggforce * imports
  • ggrepel * imports
  • ggside * imports
  • glue * imports
  • grDevices * imports
  • grid * imports
  • limma * imports
  • methods * imports
  • rlang * imports
  • rtracklayer * imports
  • scales * imports
  • stats * imports
  • stringr * imports
  • tidyr * imports
  • tidyselect * imports
  • utils * imports
  • vctrs * imports
  • BiocStyle * suggests
  • covr * suggests
  • knitr * suggests
  • plyranges * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
  • tidyverse * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite