Data

Tools

Indexes

Applications

Experiments

Open Source Science

QTLExperiment

R/Bioconductor S4 class for QTL summary statistics and metadata

https://github.com/dunstone-a/qtlexperiment

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
    4 of 7 committers (57.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.0%) to scientific vocabulary

Keywords from Contributors

genomics bioconductor-package bioconductor gene u24ca289073 rna-seq-analysis single-cell-analysis single-cell-rna-seq
Last synced: 10 months ago · JSON representation

Repository

R/Bioconductor S4 class for QTL summary statistics and metadata

Basic Info
  • Host: GitHub
  • Owner: dunstone-a
  • License: gpl-3.0
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 359 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 3 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License

README.md

QTLExperiment Package

QTLExperiment is an R container package for storing and manipulating QTL summary statistics.

Installation and Usage

This package can be installed from Bioconductor using the following code:

``` if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager")

BiocManager::install("QTLExperiment", version = "devel") ```

Using the most recent version of R is strongly recommended (R 4.4.2 at the time of writing).

There are several other packages from CRAN and Bioconductor that QTLExperiment uses, so you will need to have these packages installed as well. The CRAN packages should install automatically when QTLExperiment is installed, but you will need to install the Bioconductor packages manually.

Not all of the following are strictly necessary, but have been included here as they enhance the functionality of QTLExperiment. The commands below should help with package installations.

CRAN

{r install-cran} install.packages(c("knitr", "dplyr", "collapse", "vroom", "ashr", "tidyr", "testthat"))

Bioconductor

{r load-bioc} BiocManager::install(c("SummarizedExperiment", "BiocGenerics", "S4Vectors"))

Getting started

Get started with QTLExperiment by checking out the vignette that introduces the main features and functionality of QTLExperiment. From inside an R session, load QTLExperiment and then browse the vignettes:

library(QTLExperiment) browseVignettes("QTLExperiment")

Acknowledgements and disclaimer

The package leans heavily on previously published work and packages, namely SummarizedExperiment. The QTLE S4 class is inspired by SingleCellExperiment.

The package is currently in a Beta state. The major functionality of the package is settled, but it is still under development so may change from time to time. Please do try it and contact me with bug reports, feedback, feature requests, questions and suggestions to improve the package.

Christina Brady Del Azodi, November 2022

Owner

  • Name: Millie
  • Login: dunstone-a
  • Kind: user

GitHub Events

Total
  • Watch event: 1
  • Push event: 19
  • Create event: 3
Last Year
  • Watch event: 1
  • Push event: 19
  • Create event: 3

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 107
  • Total Committers: 7
  • Avg Commits per committer: 15.286
  • Development Distribution Score (DDS): 0.523
Past Year
  • Commits: 31
  • Committers: 5
  • Avg Commits per committer: 6.2
  • Development Distribution Score (DDS): 0.355
Top Committers
Name Email Commits
dunstone-a a****e@g****m 51
cazodi c****i@s****u 31
Amelia Dunstone a****e@s****u 16
J Wokaty j****y@s****u 4
A Wokaty a****y@s****u 2
J Wokaty j****y@u****m 2
Millie 5****a@u****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 svi.edu.au: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total 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
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
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,416 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: QTLExperiment

S4 classes for QTL summary statistics and metadata

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 4,416 Total
Rankings
Dependent repos count: 0.0%
Average: 24.7%
Forks count: 30.1%
Dependent packages count: 31.7%
Stargazers count: 36.9%
Maintainers (1)
amelia.dunstone@svi.edu.au
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • SummarizedExperiment * depends
  • BiocGenerics * imports
  • S4Vectors * imports
  • ashr * imports
  • checkmate * imports
  • collapse * imports
  • dplyr * imports
  • methods * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • utils * imports
  • vroom * imports
  • BiocStyle * suggests
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests