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mapseq

This repository provides an end-to-end open source pipeline for the processing of MAPseq (Marker Assisted Programming sequencing) data.

https://github.com/willisbillis/mapseq

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 (16.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

This repository provides an end-to-end open source pipeline for the processing of MAPseq (Marker Assisted Programming sequencing) data.

Basic Info
  • Host: GitHub
  • Owner: willisbillis
  • License: bsd-3-clause
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 17.5 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 3
Created about 2 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

MAPseq Pipeline and Analysis DOI

logo

This repository provides an end-to-end open source pipeline for the processing of MAPseq (Marker Assisted Programming sequencing) data.

Pre-Installation Requirements

Supported Operating Systems: - Ubuntu 22.04

We recommend creating a new conda environment for the installation of the tools required for the MAPseq pipeline and secondary analysis. For external software (not including Cell Ranger), we provide an environment.yml file for easy installation with conda. This can be run and initialized with:

```bash

Clone the repository

git clone https://github.com/willisbillis/MAPseq.git

or, if you have GitHub CLI installed:

gh repo clone willisbillis/MAPseq

cd MAPseq conda env create --name mapseqenv --file environment.yml conda activate mapseq_env ```

External software required

Installation

After installing necessary requirements, you may install the MAPseq pipeline from source using:

bash gh repo clone willisbillis/MAPseq cd MAPseq ./install.sh # sudo password will be prompted during this script

It is necessary to reload the shell for changes to take effect after installation. We recommend doing this by closing the current session and opening a new one.

Remove an Installation

To remove changes made by the installation, you may navigate to the MAPseq repository and revert the changes with the following:

bash cd $MAPSEQ_REPO_PATH ./uninstall.sh # sudo password will be prompted during this script

For the changes to take effect, the shell must be reloaded. We recommend doing this by closing the current session and opening a new one.

Questions and Issues

If you have a question, error, or bug to report, please use the issue page.

Resources

Citing

If you make use of this software for your work we would appreciate it if you would include the citation in any subsequent work. You may cite it using the dropdown menu in the top right of this page.

Owner

  • Name: Elliott Williams
  • Login: willisbillis
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Williams"
  given-names: "M Elliott"
  orcid: "https://orcid.org/0000-0001-8271-3394"
title: "MAPseq"
version: 0.2.1
doi: 10.5281/zenodo.10903737
date-released: 2025-07-10
url: "https://github.com/willisbillis/MAPseq"

GitHub Events

Total
  • Create event: 16
  • Release event: 1
  • Issues event: 4
  • Delete event: 15
  • Issue comment event: 13
  • Push event: 51
  • Pull request review event: 8
  • Pull request event: 28
Last Year
  • Create event: 16
  • Release event: 1
  • Issues event: 4
  • Delete event: 15
  • Issue comment event: 13
  • Push event: 51
  • Pull request review event: 8
  • Pull request event: 28

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 15
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 5 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 10
Past Year
  • Issues: 0
  • Pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.67
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 10
View more stats
Top Authors
Issue Authors
  • willisbillis (8)
Pull Request Authors
  • github-actions[bot] (34)
  • willisbillis (14)
  • dependabot[bot] (13)
Top Labels
Issue Labels
enhancement (8)
Pull Request Labels
dependencies (13)

Dependencies

.github/workflows/main.yml actions
  • actions/checkout v3 composite
  • jhutchings1/conda-dependency-submission-action v0.0.2 composite
src/mapseq_template/pipeline/ATAC.ASAP/tools/kite/setup.py pypi
environment.yaml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • bzip2 1.0.8
  • ca-certificates 2024.2.2
  • ld_impl_linux-64 2.40
  • libffi 3.4.2
  • libgcc-ng 13.2.0
  • libgomp 13.2.0
  • libnsl 2.0.1
  • libsqlite 3.45.2
  • libstdcxx-ng 13.2.0
  • libuuid 2.38.1
  • libxcrypt 4.4.36
  • libzlib 1.2.13
  • ncurses 6.4.20240210
  • openssl 3.2.1
  • pip 24.0
  • python 3.8.19
  • readline 8.2
  • setuptools 69.0.3
  • sqlite 3.45.2
  • tk 8.6.13
  • wheel 0.43.0
  • xz 5.2.6