crmetrics

Summarization of CellRanger count metrics.

https://github.com/khodosevichlab/crmetrics

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary

Last synced: 9 months ago · JSON representation

Repository

Summarization of CellRanger count metrics.

Basic Info

Host: GitHub
Owner: khodosevichlab
Language: R
Default Branch: main
Size: 19.8 MB

Statistics

Stars: 5
Watchers: 2
Forks: 1
Open Issues: 6
Releases: 3

Created about 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog

README.md

CRMetrics

05-07-2023

Cell Ranger output filtering and metrics visualisation

Installation

r install.packages("remotes") remotes::install_github("khodosevichlab/CRMetrics") # CRAN version remotes::install_github("khodosevichlab/CRMetrics", ref = "dev") # developer version

Initialization

A CRMetrics object can be initialized in different ways using CRMetrics$new(). Either data.path or cms must be provided. The most important arguments are:

data.path: A path to a directory containing sample-wise directories with outputs from cellranger count. Can also be NULL. Can also be a vector of multiple paths.
cms: A list with count matrices. Must be named with sample IDs. Can also be NULL
metadata: Can either be 1) a data.frame, or 2) a path to a table file (separator should be set with the sep.meta argument), or 3) NULL. For 1) and 2) the object must contain named columns, and one column has to be named sample containing sample IDs. Sample IDs must match the directory names in data.path or names of cms unless both these are NULL. In case of 3), a minimal metadata object is created from names in data.path or names of cms.

Vignette

For usage, please see the vignette / code.

Python integrations

CRMetrics makes use of several Python packages, some of them through the reticulate package in R, please see the included example workflow in the vignette.

Cite

To cite this work, please run citation("CRMetrics") or cite our preprint:

Fabienne Lorena Kick, Henrietta Holze, Rasmus Rydbirk, Konstantin Khodosevich: CRMetrics - an R package for Cell Ranger Filtering and Metrics Visualisation, 06 July 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-2853524/v1]

Owner

Name: Khodosevich lab
Login: khodosevichlab
Kind: organization
Location: Denmark

Website: https://www.bric.ku.dk/Research/khodosevich-group/
Repositories: 10
Profile: https://github.com/khodosevichlab

GitHub Events

Total

Issue comment event: 3
Push event: 10
Pull request review event: 34
Pull request review comment event: 34
Pull request event: 6
Fork event: 1

Last Year

Issue comment event: 3
Push event: 10
Pull request review event: 34
Pull request review comment event: 34
Pull request event: 6
Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 46
Total pull requests: 11
Average time to close issues: 14 days
Average time to close pull requests: 2 minutes
Total issue authors: 9
Total pull request authors: 2
Average comments per issue: 1.41
Average comments per pull request: 0.0
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 4
Average time to close issues: N/A
Average time to close pull requests: less than a minute
Issue authors: 1
Pull request authors: 2
Average comments per issue: 5.0
Average comments per pull request: 0.0
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

rrydbirk (19)
HenriettaHolze (15)
flkick (4)
FFriis (2)
ainsku (2)
Laura19993 (1)
XianXin0418 (1)
Gesmira (1)
aphalo (1)

Pull Request Authors

rrydbirk (10)
Laura19993 (2)

Top Labels

Issue Labels

enhancement (5) help wanted (2) bug (2) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 672 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

cran.r-project.org: CRMetrics

Cell Ranger Output Filtering and Metrics Visualization

Homepage: https://github.com/khodosevichlab/CRMetrics
Documentation: http://cran.r-project.org/web/packages/CRMetrics/CRMetrics.pdf
License: GPL-3
Latest release: 0.3.2
published over 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 672 Last month

Rankings

Forks count: 28.8%

Dependent packages count: 29.8%

Stargazers count: 31.7%

Average: 34.4%

Dependent repos count: 35.5%

Downloads: 46.1%

Maintainers (1)

rrydbirk@outlook.dk