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sequencing-data-analysis-training

SIB course that introduces analysis of NGS data

https://github.com/sib-swiss/sequencing-data-analysis-training

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
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.7%) to scientific vocabulary

Keywords

course ngs-analysis teaching training tutorial
Last synced: 6 months ago · JSON representation

Repository

SIB course that introduces analysis of NGS data

Basic Info
Statistics
  • Stars: 16
  • Watchers: 7
  • Forks: 13
  • Open Issues: 4
  • Releases: 15
Topics
course ngs-analysis teaching training tutorial
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Zenodo

README.md

build workflow GitHub Release Date DOI License: CC BY-SA 4.0

Hosted at: sib-swiss.github.io/sequencing-data-analysis-training

NGS introduction website

This website is generated with MkDocs, with the theme Material.

To host it locally, install MkDocs: bash pip install mkdocs

and Material: bash pip install mkdocs-material

Host it with: bash mkdocs serve

Check it out with your browser at http://localhost:8000/

Owner

  • Name: SIB Swiss Institute of Bioinformatics
  • Login: sib-swiss
  • Kind: organization
  • Location: Switzerland

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Delete event: 1
  • Push event: 24
  • Pull request review event: 1
  • Pull request event: 4
  • Fork event: 1
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 2
  • Delete event: 1
  • Push event: 24
  • Pull request review event: 1
  • Pull request event: 4
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 20
  • Total pull requests: 9
  • Average time to close issues: 3 months
  • Average time to close pull requests: 12 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.22
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: 3 days
  • Average time to close pull requests: 3 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • GeertvanGeest (1)
Pull Request Authors
  • GeertvanGeest (2)
  • dktanwar (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/docker-image.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
Docker/rstudio/Dockerfile docker
  • rocker/rstudio 4 build
Docker/vscode/Dockerfile docker
  • linuxserver/code-server 4.12.0 build
Docker/vscode/environment.yml conda
  • bowtie2 >=2.4.2
  • bwa >=0.7.17
  • cutadapt >=3.4
  • deeptools >=3.5
  • entrez-direct >=15
  • fastp
  • fastqc >=0.11.8
  • freebayes >=1.3.6
  • gatk4
  • hisat2 >=2.2.1
  • minimap2 >=2.18
  • multiqc
  • pip
  • samtools >=1.10
  • sra-tools >=3
  • subread >=2.0.1