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seeker

https://github.com/hugheylab/seeker

Science Score: 26.0%

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

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 2
  • Open Issues: 0
  • Releases: 2
Created almost 8 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

seeker

check-deploy codecov Netlify Status CRAN Status drat version

seeker is an R package for fetching and processing sequencing data, especially RNA-seq data, as well as microarray data. Hopefully it helps you get what you're after, before the day you die. For more details, see Schoenbachler and Hughey (2022).

Installation

To use seeker, you can install seeker and its dependencies, or use a pre-built Docker image in which seeker and its dependencies are already installed.

R package and dependencies

  1. Install the BiocManager R package.

    r if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')

  2. Install the seeker R package, either from CRAN or from the Hughey Lab drat repository. We use BiocManager::install() in order to smoothly install seeker's dependencies that are on Bioconductor.

    ```r BiocManager::install('seeker') # CRAN

    BiocManager::install('seeker', site_repository = 'https://hugheylab.github.io/drat/') # drat

    ```

  3. Install the system dependencies to fetch and process sequencing data. The simplest way to do this is to use the function installSysDeps(). For example,

    r seeker::installSysDeps('~', '~', '~', '~')

    You can also use installSysDeps() to fetch genomes from refgenie, such as those required to quantify transcript abundances using salmon.

Docker image

The Docker image is called socker and is based on rocker/rstudio.

sh docker pull ghcr.io/hugheylab/socker

Usage

For an introduction to the package, read the vignette. For more details, check out the reference documentation.

Owner

  • Name: Hughey Lab
  • Login: hugheylab
  • Kind: organization

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 22
  • Total pull requests: 25
  • Average time to close issues: 3 days
  • Average time to close pull requests: 11 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.91
  • Average comments per pull request: 5.44
  • Merged pull requests: 20
  • Bot issues: 14
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 months
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • github-actions[bot] (14)
  • JSchoenbachler (6)
  • jakejh (2)
Pull Request Authors
  • JSchoenbachler (14)
  • jakejh (8)
  • jacorvar (5)
Top Labels
Issue Labels
lint (14)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 371 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: seeker

Simplified Fetching and Processing of Microarray and RNA-Seq Data

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 371 Last month
Rankings
Forks count: 21.9%
Stargazers count: 26.2%
Dependent packages count: 29.8%
Average: 32.3%
Dependent repos count: 35.5%
Downloads: 48.1%
Maintainers (1)
jakejhughey@gmail.com
Last synced: over 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • AnnotationDbi >= 1.52.0 imports
  • ArrayExpress >= 1.50.0 imports
  • BiocManager >= 1.30.0 imports
  • GEOquery >= 2.58.0 imports
  • R.utils >= 2.11.0 imports
  • RCurl >= 1.98 imports
  • affy >= 1.68.0 imports
  • biomaRt >= 2.36.1 imports
  • checkmate >= 2.0.0 imports
  • curl >= 3.2 imports
  • data.table >= 1.11.8 imports
  • foreach >= 1.4.4 imports
  • glue >= 1.5.0 imports
  • jsonlite >= 1.7.2 imports
  • methods * imports
  • qs >= 0.21.2 imports
  • readr >= 1.4.0 imports
  • sessioninfo >= 1.2.0 imports
  • tximport >= 1.8.0 imports
  • withr >= 2.4.2 imports
  • yaml >= 2.2.1 imports
  • Biobase * suggests
  • doParallel >= 1.0.16 suggests
  • knitr * suggests
  • org.Mm.eg.db * suggests
  • rmarkdown * suggests
  • testthat >= 3.1.0 suggests