callingcardstools

A collection of objects and functions to work with calling cards sequencing tools. See docs at https://cmatkhan.github.io/callingCardsTools

https://github.com/cmatkhan/callingcardstools

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
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DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (17.3%) to scientific vocabulary

Scientific Fields

Biology Life Sciences - 84% confidence

Mathematics Computer Science - 84% confidence

Last synced: 4 months ago · JSON representation ·

Repository

A collection of objects and functions to work with calling cards sequencing tools. See docs at https://cmatkhan.github.io/callingCardsTools

Basic Info

Host: GitHub
Owner: cmatKhan
License: other
Language: Python
Default Branch: main
Homepage:
Size: 34.5 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 4
Releases: 25

Created over 3 years ago · Last pushed 10 months ago

Metadata Files

Readme Contributing License Citation

README.md

callingCardsTools

Introduction

CallingCardsTools Provides both an API and a number of cmd line tools for processing raw Calling Cards data. This is used in the nf-core/callingcards pipeline, which provides a workflow to process both yeast and mammals Calling Cards data.

Documentation

Served Documentation provides information on filetypes and the API. For help with the cmd line tools, simply install callingcardstools (see below) and do:

bash callingcardstools --help

Each of the cmd line tools also provides a --help message.

Installation

callingCardsTools is available through bioconda:

bash conda install -c bioconda callingcardstools

pypi:

bash pip install callingcardstools

or github (this will be the most current version):

bash pip install git+https://github.com/cmatkhan/callingCardsTools.git

After installing, you can get help with the cmd line tools by doing:

bash callingcardstools --help

Callingcardstools is containerized:

A singularity container is hosted on Galaxyhub. If you go to this site, make sure the 'c's have loaded and then search for 'callingcardstools'. There is a container for each version which is on bioconda. Make sure you get the correct version.
A docker container is hosted on quay (and biocontainers). Again, make sure you get the correct version.

Development Installation

install poetry

I prefer to set the default location of the virtual environment to the project directory. You can set that as a global configuration for your poetry installation like so: poetry config virtualenvs.in-project true

git clone the repo
cd into the repo and issue the command poetry install
shell into the virtual environment with poetry shell
you can pip install -e . to install the package in editable mode. This is useful if you want to test the cmd line interface as you make changes to the source code.

Owner

Name: Chase Mateusiak
Login: cmatKhan
Kind: user
Location: St Louis, MO
Company: Washington University

Website: https://mblab.wustl.edu/
Repositories: 11
Profile: https://github.com/cmatKhan

Bioinformatics Scientist in Michael Brent's lab at Washington University, St Louis

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "callingCardsTools"
doi: 10.5281/zenodo.10042067
authors:
  - name: "Mateusiak, Chase"
    orcid: "https://orcid.org/0000-0002-2890-4242"
repository-code: "https://github.com/cmatKhan/callingCardsTools"

GitHub Events

Total

Create event: 3
Release event: 1
Issues event: 6
Delete event: 2
Push event: 5
Pull request event: 4

Last Year

Create event: 3
Release event: 1
Issues event: 6
Delete event: 2
Push event: 5
Pull request event: 4

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 57
Total Committers: 1
Avg Commits per committer: 57.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
chase mateusiak	c**k@g**m	57

Issues and Pull Requests

Last synced: about 2 years ago

All Time

Total issues: 6
Total pull requests: 5
Average time to close issues: about 2 months
Average time to close pull requests: 3 minutes
Total issue authors: 2
Total pull request authors: 1
Average comments per issue: 1.33
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 5
Pull requests: 1
Average time to close issues: about 2 months
Average time to close pull requests: 16 minutes
Issue authors: 2
Pull request authors: 1
Average comments per issue: 1.6
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

cmatKhan (9)
marialexandra16 (3)

Pull Request Authors

cmatKhan (6)

Top Labels

Issue Labels

enhancement (8) bug (4) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 40 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 29
Total maintainers: 1

pypi.org: callingcardstools

A collection of objects and functions to work with calling cards sequencing tools

Homepage: https://cmatkhan.github.io/callingCardsTools/
Documentation: https://cmatkhan.github.io/callingCardsTools/
License: MIT
Latest release: 1.8.1
published 10 months ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 40 Last month

Rankings

Dependent packages count: 6.6%

Average: 27.6%

Forks count: 30.5%

Dependent repos count: 30.6%

Downloads: 31.0%

Stargazers count: 39.1%

Maintainers (1)

cmatkhan

Last synced: 4 months ago

Dependencies

poetry.lock pypi

pyproject.toml pypi

autopep8 ^1.6.0 develop
docutils ^0.19 develop
flake8 ^4.0.1 develop
ipykernel ^6.15.1 develop
pytest ^5.2 develop
Cython ^0.29.30
biopython ^1.79
bx-python ^0.8.13
numpy ^1.23.1
pandas ^1.4.3
pybedtools ^0.9.0
pysam ^0.19.1
python >=3.8,<3.11
scipy ^1.8.1

.github/workflows/build_docs.yml actions

actions/checkout v2 composite
mhausenblas/mkdocs-deploy-gh-pages master composite

.github/workflows/codecov.yml actions

actions/checkout v1 composite
actions/setup-python v2 composite
codecov/codecov-action v3 composite

.github/workflows/pyright.yml actions

jakebailey/pyright-action v1 composite

Dockerfile docker

rocker/r-ubuntu latest build