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fastqtogenecounts

This is an automated pipeline to map SRR files to gene counts

https://github.com/helikarlab/fastqtogenecounts

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

This is an automated pipeline to map SRR files to gene counts

Basic Info
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 2
  • Open Issues: 9
  • Releases: 4
Created almost 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme Citation

README.md

Fastq to Gene Counts

Code style: snakefmt

Please view the documentation for instructions on how to download, set up, and execute this pipeline.

Owner

  • Name: Digital Twin Innovation Hub
  • Login: HelikarLab
  • Kind: organization
  • Location: University of Nebraska-Lincoln

Our group focuses on the development of technologies which enable the integration of computational modelling with day-to-day work of laboratory scientists.

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: FastqToGeneCounts
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Josh
    email: jloecker3@huskers.unl.edu
    affiliation: University of Nebraska-Lincoln
    orcid: 'https://orcid.org/0000-0002-6388-2958'
    family-names: Loecker
  - given-names: Brandt
    family-names: Bessel
    orcid: 'https://orcid.org/0000-0003-2334-8790'
    email: babessell@gmail.com
    affiliation: University of Nebraska-Lincoln
repository-code: 'https://github.com/HelikarLab/FastqToGeneCounts'
keywords:
  - snakemake
  - NCBI
  - Gene Expression Omnibus
  - GEO
version: 1.0.0
date-released: '2021-09-30'

GitHub Events

Total
  • Delete event: 6
  • Push event: 8
  • Pull request event: 15
  • Create event: 7
Last Year
  • Delete event: 6
  • Push event: 8
  • Pull request event: 15
  • Create event: 7

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • JoshLoecker (19)
  • dependabot[bot] (8)
Top Labels
Issue Labels
Pull Request Labels
dependencies (8) ruby (8)

Dependencies

docs/Gemfile rubygems
  • github-pages >= 0 development
docs/Gemfile.lock rubygems
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  • coffee-script 2.4.1
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  • faraday-em_http 1.0.0
  • faraday-em_synchrony 1.0.0
  • faraday-excon 1.1.0
  • faraday-net_http 1.0.1
  • faraday-net_http_persistent 1.1.0
  • ffi 1.15.3
  • forwardable-extended 2.6.0
  • gemoji 3.0.1
  • github-pages 215
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  • zeitwerk 2.4.2