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https://github.com/csoneson/armor

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

https://github.com/csoneson/armor

Science Score: 13.0%

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    Low similarity (13.5%) to scientific vocabulary

Keywords

rna-seq workflow
Last synced: 9 months ago · JSON representation

Repository

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

Basic Info
  • Host: GitHub
  • Owner: csoneson
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 28.9 MB
Statistics
  • Stars: 164
  • Watchers: 14
  • Forks: 33
  • Open Issues: 1
  • Releases: 1
Topics
rna-seq workflow
Created over 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

ARMOR workflow

snakemake-run

ARMOR (Automated Reproducible MOdular RNA-seq) is a Snakemake workflow, aimed at performing a typical RNA-seq workflow in a reproducible, automated, and partially contained manner. It is implemented such that alternative or similar analysis can be added or removed.

ARMOR consists of a Snakefile, a conda environment file (envs/environment.yaml) a configuration file (config.yaml) and a set of R scripts, to perform quality control, preprocessing and differential expression analysis of RNA-seq data. The output can be combined with the iSEE R package to generate a shiny application for browsing and sharing the results.

By default, the pipeline performs all the steps shown in the diagram below. However, you can turn off any combination of the light-colored steps (e.g STAR alignment or DRIMSeq analysis) in the config.yaml file.

Advanced use: If you prefer other software to run one of the outlined steps (e.g. DESeq2 over edgeR, or kallisto over Salmon), you can use the software of your preference provided you have your own script(s), and change some lines within the Snakefile. If you think your "custom rule" might be of use to a broader audience, let us know by opening an issue.

Using the ARMOR workflow

Assuming that snakemake and conda are installed (and your system has the necessary libraries to compile R packages), you can use the following commands on a test dataset:

git clone https://github.com/csoneson/ARMOR.git cd ARMOR && snakemake --use-conda

To use the ARMOR workflow on your own data, follow the steps outlined in the wiki.

Workflow graph

DAG
Blue circles are rules run in R, orange circles from software called as shell commands. Dashed lines and light-colored circles are optional rules, controlled in config.yaml

Contributors

Current contributors include:

Owner

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

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 4
  • Push event: 2
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 4
  • Issue comment event: 4
  • Push event: 2
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 577
  • Total Committers: 9
  • Avg Commits per committer: 64.111
  • Development Distribution Score (DDS): 0.451
Past Year
  • Commits: 11
  • Committers: 1
  • Avg Commits per committer: 11.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Charlotte Soneson c****n@g****m 317
fionarhuang f****g@g****m 108
sorjuela s****l@g****m 65
markrobinsonuzh m****n@i****h 42
Katharina Hembach 3****h 31
markrobinsonuzh m****h 7
Katharina Hembach k****h@g****m 5
Carissa Bleker c****r 1
sorjuela s****a@g****m 1
Committer Domains (Top 20 + Academic)
imls.uzh.ch: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 52
  • Total pull requests: 52
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 days
  • Total issue authors: 13
  • Total pull request authors: 5
  • Average comments per issue: 3.54
  • Average comments per pull request: 0.23
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: 21 days
  • Average time to close pull requests: 42 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 6.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • csoneson (32)
  • markrobinsonuzh (4)
  • devang-mehta (3)
  • sorjuela (2)
  • anzezupanic (2)
  • ms-gx (2)
  • luongphekidz07 (1)
  • JuHey (1)
  • matrs (1)
  • ruqianl (1)
  • MDanialSaleem (1)
  • danylmc (1)
  • fionarhuang (1)
  • rrdavis77 (1)
Pull Request Authors
  • csoneson (32)
  • fionarhuang (10)
  • sorjuela (6)
  • markrobinsonuzh (4)
  • khembach (3)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

envs/environment.yaml conda
  • bedtools 2.30.0.*
  • cutadapt 3.2.*
  • fastqc 0.11.9.*
  • multiqc 1.9.*
  • pandoc 2.11.*
  • salmon 1.4.0.*
  • samtools 1.11.*
  • star 2.7.7a.*
  • tbb 2020.2.*
  • trim-galore 0.6.6.*
  • ucsc-bedgraphtobigwig 377.*
.github/workflows/snakemake-run.yaml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-r v2 composite
  • s-weigand/setup-conda v1.1.0 composite