ngsReports
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 7 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
8 of 13 committers (61.5%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: smped
- Language: R
- Default Branch: devel
- Homepage: https://smped.github.io/ngsReports/
- Size: 43.7 MB
Statistics
- Stars: 23
- Watchers: 7
- Forks: 4
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
ngsReports 
<!-- badges: end -->
An R Package for managing FastQC reports and other NGS related log files inside R. Except for some periodic minor bug fixes, this branch is the current release which is also available from the Bioconductor website.
Installation
To install required packages follow the instructions below.
install.packages("BiocManager")
BiocManager::install("ngsReports")
library(ngsReports)
Usage
The paper for the package can be found here. For a detailed usage guide please see here.
ShinyApp
A Graphical User Interface (Shiny App) has been developed for interactive inspection of many FastQC reports. The ngsReports shiny app can be installed here.
Tools Supported (By Category)
Quality control
- FastQC
- fastp
Adapter removal and trimming
- AdapterRemoval
- cutadapt
- trimmomatic
- fastp
Deduplication
- umi_tools dedup
Mapping and alignment
- bowtie
- bowtie2
- hisat2
- macs2 callpeak
- picard MarkDuplicates
- RNA-SeQC2
- samtools flagstat
- salmon
- STAR
Transcript/gene quantificaiton
- feature counts (Subread)
Genome assembly
- BUSCO
- quast
Citation
Please cite our paper:
@article{ward2018ngsreports,
author = {Ward, Christopher M and To, Thu-Hien and Pederson, Stephen M},
title = "{ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files}",
journal = {Bioinformatics},
year = {2019},
month = {12},
doi = {10.1093/bioinformatics/btz937},
url = {https://doi.org/10.1093/bioinformatics/btz937}
}
Owner
- Name: Stevie Pederson
- Login: smped
- Kind: user
- Location: Adelaide, Australia
- Company: Black Ochre Data Labs, Telethon Kids Institute
- Twitter: stevie_ped
- Repositories: 1
- Profile: https://github.com/smped
GitHub Events
Total
- Watch event: 1
- Push event: 4
- Create event: 2
Last Year
- Watch event: 1
- Push event: 4
- Create event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Steve Pederson | s****n@a****u | 469 |
| steveped | s****u@g****m | 157 |
| Chris | a****4@a****u | 142 |
| CMWbio | c****d@a****u | 114 |
| Steve Pederson | s****d | 39 |
| Chris | a****4@s****u | 25 |
| Nitesh Turaga | n****a@g****m | 14 |
| Chris | c****d@s****u | 13 |
| CMWbio | a****4@s****u | 8 |
| tothuhien | t****n@g****m | 7 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| Dan Kortschak | d****k@a****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 40
- Total pull requests: 5
- Average time to close issues: 2 months
- Average time to close pull requests: 2 months
- Total issue authors: 15
- Total pull request authors: 3
- Average comments per issue: 1.95
- Average comments per pull request: 1.2
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 6 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- smped (22)
- Rohit-Satyam (3)
- edgardomortiz (2)
- baerlachlan (1)
- fabio-marcelo (1)
- tothuhien (1)
- lmanchon (1)
- sa-lee (1)
- legbar (1)
- JulianSpagnuolo (1)
- Teezi (1)
- a-lud (1)
- CharlotteSai (1)
- scseekers (1)
- LaureTomas (1)
Pull Request Authors
- smped (2)
- kortschak (2)
- CMWbio (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 12,902 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: ngsReports
Load FastqQC reports and other NGS related files
- Homepage: https://github.com/smped/ngsReports
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ngsReports/inst/doc/ngsReports.pdf
- License: LGPL-3
-
Latest release: 2.10.0
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- BiocGenerics * depends
- R >= 4.1.0 depends
- ggplot2 >= 3.3.5 depends
- tibble >= 1.3.1 depends
- Biostrings * imports
- DT * imports
- checkmate * imports
- dplyr >= 1.0.0 imports
- forcats * imports
- ggdendro * imports
- grDevices >= 3.6.0 imports
- grid * imports
- lifecycle * imports
- lubridate * imports
- methods * imports
- pander * imports
- plotly >= 4.9.4 imports
- readr * imports
- reshape2 * imports
- rmarkdown * imports
- scales * imports
- stats * imports
- stringr * imports
- tidyr * imports
- tidyselect >= 0.2.3 imports
- utils * imports
- zoo * imports
- BiocStyle * suggests
- Cairo * suggests
- knitr * suggests
- testthat * suggests
- truncnorm * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite