Data

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Open Source Science

https://github.com/csoneson/alevinqc

Create QC and summary reports for Alevin output

https://github.com/csoneson/alevinqc

Science Score: 49.0%

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
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords from Contributors

transcriptomics genomics bioconductor-package bioconductor gene-expression gene mass-spectrometry proteomics single-cell single-cell-analysis
Last synced: 7 months ago · JSON representation

Repository

Create QC and summary reports for Alevin output

Basic Info
Statistics
  • Stars: 31
  • Watchers: 4
  • Forks: 6
  • Open Issues: 2
  • Releases: 0
Created over 7 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License

README.md

alevinQC

Codecov.io coverage status R build status

The alevinQC R package provides functionality for generating QC reports summarizing the output of alevin (Srivastava et al., Genome Biology 20:65 (2019)). The reports can be generated in html or pdf format, or as R/Shiny applications.

Installation:

alevinQC is available from Bioconductor, and can be installed using the BiocManager CRAN package:

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

Note that alevinQC v 1.1 or newer is required to process output from Salmon version 0.14.0 or newer.

Example usage:

alevinQCReport(baseDir = system.file("extdata/alevin_example_v0.14", package = "alevinQC"), sampleId = "testSample", outputFile = "alevinReport.html", outputFormat = "html_document", outputDir = tempdir(), forceOverwrite = TRUE)

For more information, we refer to the package vignette.

Owner

  • Name: Charlotte Soneson
  • Login: csoneson
  • Kind: user

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 8
  • Create event: 2
Last Year
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 8
  • Create event: 2

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 271
  • Total Committers: 5
  • Avg Commits per committer: 54.2
  • Development Distribution Score (DDS): 0.114
Past Year
  • Commits: 8
  • Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Charlotte Soneson c****n@g****m 240
Nitesh Turaga n****a@g****m 14
J Wokaty j****y@s****u 10
DongzeHe d****a@g****m 5
A Wokaty a****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 21
  • Total pull requests: 12
  • Average time to close issues: 23 days
  • Average time to close pull requests: about 7 hours
  • Total issue authors: 20
  • Total pull request authors: 3
  • Average comments per issue: 3.95
  • Average comments per pull request: 0.75
  • Merged pull requests: 11
  • 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: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • crazyhottommy (2)
  • LisaHagenau (1)
  • PavanKhosla (1)
  • wmacnair (1)
  • apeltzer (1)
  • PietroD (1)
  • jaclyn-taroni (1)
  • Ryan-Zhu (1)
  • csoneson (1)
  • jdrnevich (1)
  • hiraksarkar (1)
  • vswarup (1)
  • gringer (1)
  • yueli8 (1)
  • changostraw (1)
Pull Request Authors
  • csoneson (10)
  • cansavvy (1)
  • DongzeHE (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 15,507 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: alevinQC

Generate QC Reports For Alevin Output

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 15,507 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 19.0%
Downloads: 56.9%
Maintainers (1)
charlottesoneson@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • DT * imports
  • GGally * imports
  • Rcpp * imports
  • cowplot * imports
  • dplyr * imports
  • ggplot2 * imports
  • methods * imports
  • rjson * imports
  • rlang * imports
  • rmarkdown >= 2.5 imports
  • shiny * imports
  • shinydashboard * imports
  • stats * imports
  • tools * imports
  • tximport >= 1.17.4 imports
  • utils * imports
  • BiocManager * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • grimbough/bioc-actions/build-install-check v1 composite
  • grimbough/bioc-actions/run-BiocCheck v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/setup-pandoc v2 composite