decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Science Score: 23.0%
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
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 12 committers (8.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.5%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Basic Info
- Host: GitHub
- Owner: benjjneb
- Language: R
- Default Branch: master
- Homepage: https://benjjneb.github.io/decontam/
- Size: 1.25 MB
Statistics
- Stars: 162
- Watchers: 11
- Forks: 27
- Open Issues: 99
- Releases: 2
Topics
Metadata Files
README.md
Documentation
An introductory vignette demonstrating how to use the decontam package to identify contaminants.
An extensive investigation of contamination in an oral mucosal dataset, that includes evaluation of deontam results.
The manuscript introducing decontam with benchmarking demonstrating how decontam-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive associations.
More documentation available through the R help interface (e.g. ?isContaminant) and at the decontam web site.
Installation
The decontam R package is most easily installed from the Bioconductor repository. To install the most recent version of the decontam package, start R (version "3.6") and enter:
```S if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("decontam") ```
See the Bioconductor documentation for decontam for additional information.
The decontam R package is also available as a source package through github. Installation requires the ability to compile R packages. This means that R and the R tool-chain must be installed, which requires the Xcode command-line tools on Mac and Rtools on Windows.
The easiest source installation method uses the devtools package:
S
library(devtools)
devtools::install_github("benjjneb/decontam")
Other Resources
Bugs and difficulties in using decontam are welcome on the issue tracker.
Planned feature improvements are also publicly catalogued at on the "Issues" page for decontam: https://github.com/benjjneb/decontam/issues
Owner
- Name: Benjamin Callahan
- Login: benjjneb
- Kind: user
- Location: Raleigh, NC
- Company: NC State University
- Repositories: 5
- Profile: https://github.com/benjjneb
Physics -> Evolution -> Microbiome -> Bioinformatics
GitHub Events
Total
- Issues event: 14
- Watch event: 12
- Issue comment event: 34
- Pull request event: 2
- Fork event: 2
Last Year
- Issues event: 14
- Watch event: 12
- Issue comment event: 34
- Pull request event: 2
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| bcallah | b****h@P****l | 34 |
| Benjamin Callahan | b****n@g****m | 14 |
| Nitesh Turaga | n****a@g****m | 10 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Felix Ernst | f****t@o****m | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| nbokulich | n****h@g****m | 1 |
| Michael McLaren | m****2@g****m | 1 |
| bcallah | b****h@p****u | 1 |
| dave1618 | n****8@g****m | 1 |
| Darío Hereñú | m****a@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 21
- Total pull requests: 2
- Average time to close issues: 6 months
- Average time to close pull requests: 6 months
- Total issue authors: 21
- Total pull request authors: 2
- Average comments per issue: 0.33
- Average comments per pull request: 0.5
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 12
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 6 months
- Issue authors: 12
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- yd-x (1)
- CamillePhilippeSCI (1)
- shwetha141 (1)
- hjarnek (1)
- anya-mueller (1)
- Skirnir3141 (1)
- mya-darsan (1)
- OluchiAroh (1)
- JayalalKJ (1)
- kx11jkjk (1)
- zztin (1)
- sihanbu (1)
- nadeaujay (1)
- Ivy-ops (1)
- Kudzai-H (1)
Pull Request Authors
- TuomasBorman (1)
- Zarzarn95 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.4.1 depends
- methods >= 3.4.1 depends
- ggplot2 >= 2.1.0 imports
- reshape2 >= 1.4.1 imports
- stats * imports
- BiocStyle * suggests
- knitr * suggests
- phyloseq * suggests
- rmarkdown * suggests