dada2
Accurate sample inference from amplicon data with single nucleotide resolution
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
✓DOI references
Found 9 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
6 of 32 committers (18.8%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Accurate sample inference from amplicon data with single nucleotide resolution
Basic Info
- Host: GitHub
- Owner: benjjneb
- License: lgpl-3.0
- Language: R
- Default Branch: master
- Homepage: http://benjjneb.github.io/dada2/
- Size: 468 MB
Statistics
- Stars: 516
- Watchers: 38
- Forks: 154
- Open Issues: 167
- Releases: 14
Topics
Metadata Files
README.md
dada2
Exact sample inference from high-throughput amplicon data. Resolves real variants differing by as little as one nucleotide. Visit the DADA2 website for the most detailed and up-to-date documentation.
Installation
The dada2 package binaries are available through Bioconductor:
```S
try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("dada2") ```
In order to install dada2 from source (and get the latest and greatest new features) see our installation from source instructions.
Documentation
The tutorial walkthrough of the DADA2 pipeline on paired end Illumina Miseq data.
Further documentation is available on the DADA2 front page.
DADA2 Articles
DADA2: High resolution sample inference from Illumina amplicon data. Nature Methods, 2016. (Open Access link.)
Other Resources
Planned feature improvements are publicly catalogued at the main DADA2 development site on github, specifically on the "Issues" page for DADA2:
https://github.com/benjjneb/dada2/issues
If the feature you are hoping for is not listed, you are welcome to add it as a feature request "issue" on this page. This request will be publicly available and listed on the page.
Bugs and difficulties in using DADA2 are also welcome on the issue tracker.
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: 137
- Watch event: 44
- Issue comment event: 391
- Push event: 13
- Pull request event: 4
- Pull request review event: 2
- Fork event: 11
Last Year
- Issues event: 137
- Watch event: 44
- Issue comment event: 391
- Push event: 13
- Pull request event: 4
- Pull request review event: 2
- Fork event: 11
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| benjjneb | b****n@g****m | 436 |
| bcallah | b****h@P****l | 135 |
| Gene Blanchard | g****4@g****m | 38 |
| Nitesh Turaga | n****a@g****m | 16 |
| Paul J. McMurdie | j****1@g****m | 14 |
| Paul J. McMurdie | m****e@a****u | 14 |
| Ben Callahan | b****h@n****u | 6 |
| Fan Li | f****b | 4 |
| Dan Tenenbaum | d****a@f****g | 4 |
| Herve Pages | h****s@f****g | 4 |
| J Wokaty | j****y@s****u | 4 |
| Hervé Pagès | h****s@f****g | 3 |
| Wojtek Bazant | w****t@v****u | 3 |
| bcallah | b****h@p****t | 3 |
| bcallah | b****h@p****u | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| zachcp | z****p@r****u | 1 |
| Dogrinev | 6****v | 1 |
| Vladimir Mikryukov | v****k | 1 |
| brendanf | b****x@g****m | 1 |
| Michael McLaren | m****2@g****m | 1 |
| Martin Morgan | m****n@f****g | 1 |
| LiNk-NY | m****9@g****m | 1 |
| Kayla-Morrell | k****l@r****g | 1 |
| I-Hsuan Lin | y****l@g****m | 1 |
| Florentin Constancias | f****s@g****m | 1 |
| Fan Li | f****b@g****m | 1 |
| Emanuel Heitlinger | e****r@g****m | 1 |
| and 2 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 487
- Total pull requests: 6
- Average time to close issues: 11 months
- Average time to close pull requests: 5 months
- Total issue authors: 369
- Total pull request authors: 5
- Average comments per issue: 4.43
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 122
- Pull requests: 3
- Average time to close issues: 20 days
- Average time to close pull requests: 19 days
- Issue authors: 99
- Pull request authors: 2
- Average comments per issue: 1.9
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- emankhalaf (10)
- marwa38 (7)
- benjjneb (7)
- luigallucci (7)
- andrebolerbarros (7)
- Danyang1111 (6)
- Ecotone23 (6)
- hjarnek (5)
- akspat (4)
- lcamVz (4)
- otaviolovison (4)
- jspychalla (4)
- Guillermouceda (4)
- MadsBjornsen (4)
- ep142 (4)
Pull Request Authors
- ycl6 (2)
- Micro-Biology (2)
- cylyau (1)
- leholman (1)
- rabdill (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 795,009 total
- Total dependent packages: 2
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: dada2
Accurate, high-resolution sample inference from amplicon sequencing data
- Homepage: http://benjjneb.github.io/dada2/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/dada2/inst/doc/dada2.pdf
- License: LGPL-2
-
Latest release: 1.36.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- Rcpp >= 0.12.0 depends
- methods >= 3.4.0 depends
- BiocGenerics >= 0.22.0 imports
- Biostrings >= 2.42.1 imports
- IRanges >= 2.6.0 imports
- RcppParallel >= 4.3.0 imports
- ShortRead >= 1.32.0 imports
- XVector >= 0.16.0 imports
- ggplot2 >= 2.1.0 imports
- parallel >= 3.2.0 imports
- reshape2 >= 1.4.1 imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests