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damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

https://github.com/niekwit/damid-seq

Science Score: 67.0%

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
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary

Keywords

bioinformatics-pipeline damid snakemake-workflow
Last synced: 6 months ago · JSON representation ·

Repository

DamMapper: Snakemake workflow for DamID-Seq analysis

Basic Info
  • Host: GitHub
  • Owner: niekwit
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 83.3 MB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 4
Topics
bioinformatics-pipeline damid snakemake-workflow
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

DamMapper

Snakemake Tests Documentation Status DOI

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

Aim

DamMapper is a containerized Snakemake pipeline for reproducible and scalable analysis of single/paired-end DamID short read Illumina data.

Documentation

Documentation of how to use DamMapper can be found at https://damid-seq.readthedocs.io/en/latest/.

Overview of documentation

  • DamID
    • DamID principle
    • Experimental considerations
  • Software requirements
    • Conda/Mamba
    • Snakemake
    • Apptainer
    • Snakefetch
  • Usage
    • Preparing raw sequencing data
    • Sample meta data and analysis settings
    • Configuration of Snakemake
    • Dry-run of the analysis
    • Visualization of the workflow
    • Running the analysis
    • Report of the results
    • Archive of the analysis
  • Output files
    • Quality control
    • Visualization of damid data
    • Peak-related plots
  • Citation
    • Workflow
    • Software used in workflow
  • literature
    • DamID
  • Source code
    • Reporting issues

Owner

  • Name: Niek Wit
  • Login: niekwit
  • Kind: user
  • Location: Cambridge, UK
  • Company: University of Cambridge

Bioinformatician @ University of Cambridge working in the labs of Prof. James Nathan and Prof. Paul Lehner

Citation (CITATION.cff) 

cff-version: 1.2.0
title: damidseq
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Niek
    family-names: Wit
    email: nw416@cam.ac.uk
    affiliation: University of Cambridge
    orcid: https://orcid.org/0009-0002-4330-5333
repository-code: 'https://github.com/niekwit/damid-seq'
license: MIT
doi: 10.5281/zenodo.10737672

GitHub Events

Total
  • Watch event: 1
  • Push event: 16
  • Create event: 1
Last Year
  • Watch event: 1
  • Push event: 16
  • Create event: 1

Dependencies

.github/workflows/conventional-prs.yml actions
  • amannn/action-semantic-pull-request v3.4.0 composite
.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • github/super-linter v4 composite
  • snakemake/snakemake-github-action v1.25.1 composite
.github/workflows/release-please.yml actions
  • GoogleCloudPlatform/release-please-action v2 composite
.docker/v0.5.0/Dockerfile docker
  • condaforge/mambaforge latest build
docs/requirements.txt pypi
  • sphinx ==7.3.7
  • sphinx_rtd_theme ==2.0.0
.docker/v0.6.0/Dockerfile docker
  • condaforge/mambaforge latest build