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qcmetrics

An R framework for quality control

https://github.com/lgatto/qcmetrics

Science Score: 23.0%

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    1 of 19 committers (5.3%) from academic institutions
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    Low similarity (7.9%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor proteomics mass-spectrometry proteomics-data spatial-proteomics visualisation genomics metabolomics proteomexchange
Last synced: 10 months ago · JSON representation

Repository

An R framework for quality control

Basic Info
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Created almost 13 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog

README.md

A General Framework for Quality Control Metrics

About

The qcmetrics package provides a general framework to develope quality control (QC) pipelines for any type of data that can be imported into R. The application of qcmetrics can be schematised in 5 points

  1. Identify a set of quality metrics of interest and implement them and their visualisation method into individual QcMetric instances.
  2. Bundles the QcMetric items into a QcMetrics instance.
  3. Automatically generate reports in pdf of html using the qcReport function using the QcMetrics object of step 2 as input.
  4. Optionally, reports can be customised.
  5. Wrap the above steps into a wrapper function or a new QC package for production use.

QC pipelines and packages will be described and disseminated through the wiki.

Installation

qcmetrics is a Bioconductor package and should in installed with

r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("qcmetrics")

Bugs and question

Either file a GitHub issue or use the Bioconductor support forum.

Owner

  • Name: Laurent Gatto
  • Login: lgatto
  • Kind: user
  • Location: Belgium
  • Company: de Duve Institute, UCLouvain

Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 242
  • Total Committers: 19
  • Avg Commits per committer: 12.737
  • Development Distribution Score (DDS): 0.595
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Laurent l****o@g****m 98
Laurent l****0@c****k 35
Laurent Gatto l****o@d****e 22
l.gatto l****o@b****8 21
Dan Tenenbaum d****a@f****g 14
d.tenenbaum d****m@b****8 14
Laurent Gatto l****o@u****e 10
Nitesh Turaga n****a@g****m 10
Herve Pages h****s@f****g 4
vobencha v****a@g****m 2
vobencha v****n@r****g 2
aoles a****s@g****m 2
Hervé Pagès h****s@f****g 2
Marc Carlson m****n@f****g 1
Sonali Arora s****a@f****g 1
LiNk-NY m****9@g****m 1
m.carlson m****n@b****8 1
Kayla-Morrell k****l@r****g 1
s.arora s****a@b****8 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 roswellpark.org: 2 fredhutch.org: 1 uclouvain.be: 1 dnavision.be: 1 cam.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 2
  • Total pull requests: 3
  • Average time to close issues: almost 4 years
  • Average time to close pull requests: about 1 year
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • Kohze (1)
  • lgatto (1)
Pull Request Authors
  • Kohze (2)
  • aoles (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 25,385 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: qcmetrics

A Framework for Quality Control

  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 25,385 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 12.5%
Downloads: 37.4%
Maintainers (1)
laurent.gatto@uclouvain.be
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3 depends
  • Biobase * imports
  • S4Vectors * imports
  • knitr * imports
  • methods * imports
  • pander * imports
  • tools * imports
  • xtable * imports
  • BiocStyle * suggests
  • MSnbase * suggests
  • affy * suggests
  • ggplot2 * suggests
  • lattice * suggests
  • mzR * suggests
  • rmarkdown * suggests
.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite