OUTRIDER
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
Science Score: 67.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
9 of 17 committers (52.9%) from academic institutions -
✓Institutional organization owner
Organization gagneurlab has institutional domain (www.gagneurlab.in.tum.de) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.6%) to scientific vocabulary
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Repository
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
Basic Info
Statistics
- Stars: 53
- Watchers: 11
- Forks: 14
- Open Issues: 15
- Releases: 8
Topics
Metadata Files
README.md
OUTRIDER
OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples. The method is published in the AJHG and available through Bioconductor. It is also part of the workflow DROP, which is described in Nature Protocols.
Please cite our method paper if you use it in a publication:
Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. Am J Hum Genet. 2018;103(6):907-917. https://doi.org/10.1016/j.ajhg.2018.10.025
Since v. 1.26.2, OUTRIDER uses the Optimal Hard Threshold algorithm to determine the optimal encoding dimension q.
Installation
OUTRIDER is an R software package requiring a running R 3.6 version or higher.
We will use BiocManager to install the package and its dependencies. If you
want to install the devel version of OUTRIDER, please install it
with devtools from GitHub directly (see below).
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install('OUTRIDER')
If you have dependency issues while installing any package, please have a look at the Troubleshooting section or submit an issue on GitHub.
OUTRIDER development installation
If you want to get the latest
development version of OUTRIDER, you can install it from GitHub with
devtools. For this, you need a working development environment to compile the
C++ code (see for details: Windows
or MacOS X).
``` install.packages('devtools')
latest development version
devtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)
installing a specific version/tag of OUTRIDER
devtools::install_github('gagneurlab/OUTRIDER@1.22.0', dependencies=TRUE) ```
To check which versions/tags are available you can check the GitHub repo here.
Quick tour through OUTRIDER
To get started with OUTRIDER, please have a look at our
vignette.
In order to get the pdf version, please type the following code in an R session:
library(OUTRIDER)
vignette('OUTRIDER')
Toubleshooting
Missing libraries while compiling R packages
On some Linux distributions we need the developer libraries for compiling the R packages.
To install those packages, please run as administrator:
For Ubuntu or debian based systems:
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmariadbd-dev
For centOS or RHEL based systems:
sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel
Owner
- Name: Gagneur lab
- Login: gagneurlab
- Kind: organization
- Website: www.gagneurlab.in.tum.de
- Repositories: 18
- Profile: https://github.com/gagneurlab
To understand the genetic basis of gene regulation and its implication in diseases.
GitHub Events
Total
- Create event: 9
- Release event: 1
- Issues event: 5
- Watch event: 5
- Delete event: 12
- Issue comment event: 14
- Push event: 30
- Pull request review comment event: 5
- Pull request review event: 9
- Pull request event: 11
- Fork event: 3
Last Year
- Create event: 9
- Release event: 1
- Issues event: 5
- Watch event: 5
- Delete event: 12
- Issue comment event: 14
- Push event: 30
- Pull request review comment event: 5
- Pull request review event: 9
- Pull request event: 11
- Fork event: 3
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Christian Mertes | m****s@i****e | 232 |
| brechtma | b****a@i****e | 112 |
| Smith Nicholas | s****h@i****e | 21 |
| Ines Scheller | s****r@i****e | 15 |
| Nitesh Turaga | n****a@g****m | 14 |
| Vicente | y****z@i****e | 5 |
| Michaela Mueller | m****r@t****e | 4 |
| nickhsmith | s****h@g****m | 4 |
| loipfins | l****s@i****e | 3 |
| Vicente Yepez | 3****8 | 2 |
| LiNk-NY | m****9@g****m | 2 |
| J Wokaty | j****y@s****u | 2 |
| AtaJadidAhari | a****i@g****m | 2 |
| vobencha | v****a@g****m | 2 |
| Hervé Pagès | h****s@f****g | 1 |
| Kayla-Morrell | k****l@r****g | 1 |
| Michaela Müller | m****e@i****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 38
- Total pull requests: 40
- Average time to close issues: 6 months
- Average time to close pull requests: 27 days
- Total issue authors: 30
- Total pull request authors: 8
- Average comments per issue: 3.08
- Average comments per pull request: 0.23
- Merged pull requests: 37
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 6
- Average time to close issues: 2 months
- Average time to close pull requests: about 11 hours
- Issue authors: 4
- Pull request authors: 3
- Average comments per issue: 5.5
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- c-mertes (3)
- naumenko-sa (3)
- lemdcock (2)
- xuwenjian85 (2)
- zyyy97 (2)
- m-pauper (2)
- pkothiyal (1)
- nickhsmith (1)
- iaradsouza1 (1)
- ellango85 (1)
- J-Lye (1)
- ktmf1991 (1)
- yhoogstrate (1)
- ccasar (1)
- hanxuelian (1)
Pull Request Authors
- c-mertes (19)
- andrearaithel (10)
- AtaJadidAhari (8)
- nickhsmith (7)
- ischeller (5)
- vyepez88 (3)
- brechtmann (1)
- loipf (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 23,547 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
bioconductor.org: OUTRIDER
OUTRIDER - OUTlier in RNA-Seq fInDER
- Homepage: https://github.com/gagneurlab/OUTRIDER
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf
- License: file LICENSE
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Latest release: 1.26.3
published 6 months ago
Rankings
Maintainers (1)
Dependencies
- BiocParallel * depends
- GenomicFeatures * depends
- R >= 3.6 depends
- SummarizedExperiment * depends
- data.table * depends
- methods * depends
- BBmisc * imports
- BiocGenerics * imports
- DESeq2 >= 1.16.1 imports
- GenomicRanges * imports
- IRanges * imports
- PRROC * imports
- RColorBrewer * imports
- Rcpp * imports
- S4Vectors * imports
- generics * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- heatmaply * imports
- matrixStats * imports
- pcaMethods * imports
- pheatmap * imports
- plotly * imports
- plyr * imports
- reshape2 * imports
- scales * imports
- splines * imports
- stats * imports
- utils * imports
- AnnotationDbi * suggests
- BiocStyle * suggests
- RMariaDB * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- beeswarm * suggests
- covr * suggests
- knitr * suggests
- org.Hs.eg.db * suggests
- rmarkdown * suggests
- testthat * suggests
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-tinytex v2 composite