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baltica

Baltica: integrated differential junction usage

https://github.com/dieterich-lab/baltica

Science Score: 49.0%

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
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords

alternative-splicing bioinformatics bioinformatics-pipeline data-integration workflows
Last synced: 6 months ago · JSON representation

Repository

Baltica: integrated differential junction usage

Basic Info
Statistics
  • Stars: 10
  • Watchers: 3
  • Forks: 3
  • Open Issues: 8
  • Releases: 4
Topics
alternative-splicing bioinformatics bioinformatics-pipeline data-integration workflows
Created about 8 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License Citation

README.md

Baltica

Zenodo DOI
bioRxiv pre-print

Baltica: integrated splice junction usage analysis

Features

  • Snakemake workflows for DJU: JunctionSeq, Majiq, rMATS, and Leafcutter
  • Snakemake workflow for de novo transcriptome annotation with Stringtie
  • Process, integrate and annotate the results from the methods
  • Summarise AS class of differently spliced junctions
  • DJU method benchmarks
  • Report on the integrative analysis

Instructions for using Baltica

We tested the instruction below in a computer cluster running Debian Linux distribution and using the Slurm job scheduler. Baltica uses Snakemake and Singularity, which support many different high-performance systems, for instructions on how to use it on different systems, please see Setting up Baltica: long edition or contact us,

Documentation

https://dieterich-lab.github.io/Baltica/.

Setting up Baltica

Instalation instructions

Contribution

Feedback and contribution are welcome. Would you mind submitting via the GitHub issue tracker Please provide the following information while submitting issue reports:

  • Software and operation system versions
  • Command-line call
  • If possible, also provide sample data so we can try to reproduce the error

Owner

  • Name: Dieterich Lab
  • Login: dieterich-lab
  • Kind: organization
  • Email: contact@dieterichlab.org
  • Location: Heidelberg, Germany

Section of Bioinformatics and Systems Cardiology at the University Hospital Heidelberg

GitHub Events

Total
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 44
  • Fork event: 1
Last Year
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 44
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 28 days
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 8.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 28 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 8.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • AlessandraLongo (2)
  • tbrittoborges (1)
  • santataRU (1)
Pull Request Authors
Top Labels
Issue Labels
question (1)
Pull Request Labels

Dependencies

.github/workflows/docker_build.yaml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
docker/baltica/1.0/Dockerfile docker
  • bioconductor/bioconductor_docker latest build
docker/junctionseq/1.16.0/Dockerfile docker
  • bioconductor/bioconductor_docker RELEASE_3_10 build
docker/leafcutter/0.2.7/Dockerfile docker
  • mambaorg/micromamba 0.13.1 build
docker/majiq/2.2/Dockerfile docker
  • python 3.7 build
docker/qc/1.0/Dockerfile docker
  • mambaorg/micromamba 0.13.1 build
docker/rmats/4.1.1/Dockerfile docker
  • mambaorg/micromamba 0.13.1 build
docker/stringtie/2.1.5/Dockerfile docker
  • debian latest build
requirements.txt pypi
  • PyYAML *
  • click *
  • snakemake >=6