Data

Tools

Indexes

Applications

Experiments

Open Source Science

mitoClone2

BioC Package Version

https://github.com/benstory/mitoclone2

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.1%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

BioC Package Version

Basic Info
  • Host: GitHub
  • Owner: benstory
  • Language: C++
  • Default Branch: main
  • Size: 1.45 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Created almost 5 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog

README.md

mitoClone2

The R package is used for performing the analysis of clonal heterogeneity based on nuclear and mitochondrial mutations in single cell RNA or DNA sequencing.

You can read about the package and explore an extensive vignette in the supplemental section of our accompanying publication:

Story B, Velten L, Mönke G, Annan A, Steinmetz L. Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants. NAR Genomics and Bioinformatics. 2024;6(3):lqae095. Published 2024 Aug 9. doi:10.1093/nargab/lqae095

1. System Requirements:

  • Linux/Mac
  • R 4.0+
  • SCITE/PhISCS (included)
  • Python 2.7, 3.6, or 3.7 (optional)

Importantly, depending on the user's need for tree-building, an installation of PhiSCS may be necessary. For SCITE, the program should be installed automatically when the mitoClone2 package is installed. Please read the manual provided by the software authors SCITE Installation Instructions to better understand the software.

See DESCRIPTION file for specific R package requirements.

The software has been successfully implemented and tested using: Python 3.6.5, R 4.0.0, and on Ubuntu 18.04, CentOS 7, macOS 14.5, and Windows 11.

2. Installation

For manual package installation use the command:

``` r

install via Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('mitoClone2')

use devtools to install

devtools::install_github("benstory/mitoClone2")

```

Estimated installation time: < 1 hour*

3. Demo

Please see R vignettes for further instructions and a demo using real data. Use the command vignette("mitoClone2") after loading the library (see Instructions) to list all available tutorials.

Estimated demo completion time: < 1 hour

4. Usage Instructions

After installing all dependencies, open an R session and load the library using the following command:

r library(mitoClone2)

Notes: Please make sure to set your environmental python variables correctly for use of gurobi. See for example the python_env parameter.

Again please view the R vignettes for usage possibilities.

  • overview: Instructions on how to filter mitochondrial mutations using either a list of sites to be excluded or shared mutations across samples/patients (typical runtime: > 10 minutes)
  • clustering: Instructions on how to cluster mutations into a clonal hierarchy and how to assign cells to clones (typical runtime: < 1 hour)

Owner

  • Login: benstory
  • Kind: user
  • Location: Heidelberg, Germany

GitHub Events

Total
  • Issues event: 6
  • Issue comment event: 9
  • Push event: 15
  • Create event: 1
Last Year
  • Issues event: 6
  • Issue comment event: 9
  • Push event: 15
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 18
  • Total Committers: 2
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.056
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Ben Story s****y@e****e 17
benstory b****y 1
Committer Domains (Top 20 + Academic)
embl.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 7
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 7
  • Total pull request authors: 0
  • Average comments per issue: 1.57
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 2.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Xiangning-Dong (1)
  • Joyjoyjoyc (1)
  • benstory (1)
  • xinghua1001 (1)
  • LiuCanidk (1)
  • smzt (1)
  • ashokpatowary (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,956 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: mitoClone2

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,956 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 18.4%
Average: 28.6%
Stargazers count: 33.2%
Downloads: 91.6%
Maintainers (1)
story.benjamin@gmail.com
Last synced: 7 months ago