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bamsignals

R package to quickly obtain count vectors from indexed bam files

https://github.com/lamortenera/bamsignals

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
    5 of 21 committers (23.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.7%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages genomics gene proteomics bioconductor metabolomics looking-for-maintainer hdf5 rhdf5 chip-profiles
Last synced: 11 months ago · JSON representation

Repository

R package to quickly obtain count vectors from indexed bam files

Basic Info
  • Host: GitHub
  • Owner: lamortenera
  • Language: R
  • Default Branch: master
  • Size: 5.95 MB
Statistics
  • Stars: 15
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

bamsignals

R package to quickly obtain count vectors from indexed bam files.

Installation

Install the devtools package to be able to directly install R packages hosted on github :

R install.packages("devtools")

To install bamsignals type:

R devtools::install_github("lamortenera/bamsignals")

Alternatively, you can install it from Bioconductor (the two repos are synchronized):

R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("bamsignals")

Owner

  • Name: Alessandro Mammana
  • Login: lamortenera
  • Kind: user

GitHub Events

Total
  • Issues event: 5
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 7
  • Push event: 4
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 5
  • Watch event: 3
  • Delete event: 1
  • Issue comment event: 7
  • Push event: 4
  • Pull request review event: 1
  • Pull request event: 6
  • Fork event: 1
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 173
  • Total Committers: 21
  • Avg Commits per committer: 8.238
  • Development Distribution Score (DDS): 0.815
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alessandro Mammana m****a@a****e 32
Johannes Helmuth h****h@m****e 32
Alessandro Mammana m****a@z****e 14
lamortenera a****r@g****m 13
Alessandro Mammana m****a@m****e 12
a.mammana a****a@b****8 12
Dan Tenenbaum d****a@f****g 11
Nitesh Turaga n****a@g****m 10
Hervé Pagès h****s@f****g 5
Bioconductor Git-SVN Bridge b****c@b****g 4
Herve Pages h****s@f****g 4
Johannes Helmuth j****h@l****m 4
Nathaniel Hayden n****n@f****g 4
d.tenenbaum d****m@b****8 4
n.hayden n****n@b****8 4
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Alessandro Mammana m****a@g****e 1
LiNk-NY m****9@g****m 1
Sonali Arora s****a@f****g 1
s.arora s****a@b****8 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 molgen.mpg.de: 2 geniux.molgen.mpg.de: 1 roswellpark.org: 1 laborberlin.com: 1 bioconductor.org: 1 fredhutch.org: 1 zoophobie.molgen.mpg.de: 1 antipasti.molgen.mpg.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 22
  • Total pull requests: 7
  • Average time to close issues: 10 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 11
  • Total pull request authors: 2
  • Average comments per issue: 2.59
  • Average comments per pull request: 0.43
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 2 months
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 6.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • your-highness (8)
  • lamortenera (4)
  • AliciaSchep (2)
  • xiaoyonf (1)
  • pkerbs (1)
  • yancychy (1)
  • ar00 (1)
  • hagen-wende (1)
  • lshep (1)
  • tomateba (1)
  • itsvenu (1)
Pull Request Authors
  • your-highness (8)
  • sanchit-saini (2)
Top Labels
Issue Labels
enhancement (2) bug (1) wontfix (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 118,935 total
  • Total dependent packages: 7
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: bamsignals

Extract read count signals from bam files

  • Versions: 5
  • Dependent Packages: 7
  • Dependent Repositories: 0
  • Downloads: 118,935 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 4.6%
Downloads: 13.9%
Maintainers (1)
johannes.helmuth@laborberlin.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • BiocGenerics * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Rcpp >= 0.10.6 imports
  • methods * imports
  • zlibbioc * imports
  • BiocStyle * suggests
  • Rsamtools * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 0.9 suggests