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affxparser

🔬 R package: This is the Bioconductor devel version of the affxparser package.

https://github.com/henrikbengtsson/affxparser

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 19 committers (21.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

bioconductor package r

Keywords from Contributors

genomics bioconductor-package gene looking-for-maintainer bioinformatics rhdf5 hdf5 mass-spectrometry ncbi-geo metabolomics
Last synced: 6 months ago · JSON representation

Repository

🔬 R package: This is the Bioconductor devel version of the affxparser package.

Basic Info
Statistics
  • Stars: 8
  • Watchers: 3
  • Forks: 3
  • Open Issues: 12
  • Releases: 0
Topics
bioconductor package r
Created over 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme Contributing

README.md

Bioconductor since badge Bioconductor build status Bioconductor build status R CMD check status Coverage Status

affxparser: Affymetrix File Parsing SDK

Installation

R package affxparser is available on Bioconductor and can be installed in R as:

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

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use: r remotes::install_github("HenrikBengtsson/affxparser", ref="develop") This will install the package from source. Because of this and because this package also compiles native code, Windows users need to have Rtools installed and macOS users need to have Xcode installed.

Development workflow

The Bioconductor development version of the affxparser package is available at https://bioconductor.org/packages/devel/bioc/html/affxparser.html. Bioconductor builds and checks this development version based on the source code in the devel branch of the package Git repository available at https://code.bioconductor.org/browse/affxparser/devel/.

The master branch of this GitHub repository is is manually kept in sync with the devel branch on the Bioconductor Git repository. If there's an update made directly to the Bioconductor devel branch, we merge it into the master branch on GitHub. Vice versa, if there are updates to the GitHub master branch, we merge those into the devel branch on Bioconductor.

The most common, and recommend workflow is to develop toward GitHub instead of directly toward the Bioconductor servers. By working toward GitHub first, we get instant checking of the code across different operating systems and R versions on GitHub Actions. This way, we can validate the code immediately, instead of having to way 24-36 hours for it to be validated on the Bioconductor check servers.

Contributing

To contribute to this package, please see CONTRIBUTING.md.

Owner

  • Name: Henrik Bengtsson
  • Login: HenrikBengtsson
  • Kind: user
  • Company: UCSF

Assoc Professor. R Foundation. R Consortium. Many R packages, e.g. future & matrixStats.

GitHub Events

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

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 563
  • Total Committers: 19
  • Avg Commits per committer: 29.632
  • Development Distribution Score (DDS): 0.49
Past Year
  • Commits: 21
  • Committers: 2
  • Avg Commits per committer: 10.5
  • Development Distribution Score (DDS): 0.19
Top Committers
Name Email Commits
Henrik Bengtsson hb@m****e 287
Kasper D. Hansen k****n@s****u 127
James Bullard b****d@b****u 38
Dan Tenenbaum d****a@f****g 24
Nitesh Turaga n****a@g****m 14
Herve Pages h****s@f****g 14
Robert Gentleman r****m@f****g 11
J Wokaty j****y@s****u 10
Patrick Aboyoun u****n 10
Kasper Daniel Hansen k****n@g****m 7
Seth Falcon s****n@f****g 6
Martin Morgan m****n@f****g 5
Hervé Pagès h****s@f****g 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
Benilton Carvalho b****h@j****u 1
Chao-Jen Wong c****2@f****g 1
Ting-Yuan Liu t****u@f****g 1
LiNk-NY m****9@g****m 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 7 jhsph.edu: 1 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1 berkeley.edu: 1 stat.berkeley.edu: 1 maths.lth.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 46
  • Total pull requests: 5
  • Average time to close issues: 6 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 9
  • Total pull request authors: 4
  • Average comments per issue: 3.57
  • Average comments per pull request: 0.8
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • HenrikBengtsson (34)
  • kasperdanielhansen (5)
  • kmclough (1)
  • zroger49 (1)
  • starsareintherose (1)
  • Christopher-Yang-Chq (1)
  • martin-g (1)
  • deepstop (1)
  • arubio2 (1)
  • drhmoosavi (1)
Pull Request Authors
  • deepstop (2)
  • HenrikBengtsson (1)
  • kasperdanielhansen (1)
  • jimhester (1)
Top Labels
Issue Labels
bug (14) help wanted (13) enhancement (11) MS Windows (4) question (2) invalid (1)
Pull Request Labels
MS Windows (2)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 361,615 total
  • Total dependent packages: 10
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: affxparser

Affymetrix File Parsing SDK

  • Versions: 5
  • Dependent Packages: 10
  • Dependent Repositories: 0
  • Downloads: 361,615 Total
Rankings
Downloads: 0.0%
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
kasperdanielhansen@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check-valgrind.yaml actions
  • actions/cache v1 composite
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v1 composite
.github/workflows/covr.yaml actions
  • actions/cache v1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
DESCRIPTION cran
  • R >= 2.14.0 depends
  • AffymetrixDataTestFiles * suggests
  • R.oo >= 1.22.0 suggests
  • R.utils >= 2.7.0 suggests