DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Science Score: 13.0%
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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Basic Info
- Host: GitHub
- Owner: lpantano
- License: mit
- Language: R
- Default Branch: main
- Homepage: http://lpantano.github.io/DEGreport/
- Size: 51.7 MB
Statistics
- Stars: 25
- Watchers: 4
- Forks: 17
- Open Issues: 16
- Releases: 1
Topics
Metadata Files
README.md
DEGreport
QCs, figures and analyses after differential expression with DESeq2 or other similar tool.
Pantano L (2017). DEGreport: Report of DEG analysis. R package version 1.13.8.
DOI: 10.18129/B9.bioc.DEGreport
Installation
This is an R package.
Bioconductor stable version
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("DEGreport")
Bioconductor latest version
r
devtools::install_git("https://git@git.bioconductor.org/packages/DEGreport")
devtools unstable version
r
install.packages("devtools")
devtools::install_github("lpantano/DEGreport")
Load the package and learn what to do:
browseVignettes("DEGreport")
Here is the last devel vignette.
Owner
- Name: Lorena Pantano
- Login: lpantano
- Kind: user
- Location: Boston
- Website: http://lpantano.github.io
- Repositories: 45
- Profile: https://github.com/lpantano
PhD in miRNA analysis in mental disease @ CRG, Barcelona, Spain. Experience in NGS data analysis. Love python, R, and data integration. twitter:@lopantano
GitHub Events
Total
- Issues event: 2
- Watch event: 3
- Issue comment event: 2
- Fork event: 1
Last Year
- Issues event: 2
- Watch event: 3
- Issue comment event: 2
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lorena Pantano | l****o@g****m | 386 |
| l.pantano | l****o@b****8 | 57 |
| Nitesh Turaga | n****a@g****m | 14 |
| Victor Barrera | B****c@g****m | 12 |
| Dan Tenenbaum | d****a@f****g | 12 |
| d.tenenbaum | d****m@b****8 | 12 |
| Lorena Pantano | l****a@v****e | 7 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 5 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 4 |
| Herve Pages | h****s@f****g | 4 |
| idelvall | n****o@b****o | 3 |
| Lorena Pantano | l****o@a****m | 3 |
| roryk | r****r@g****m | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| Lorena Pantano | l****o@d****) | 2 |
| vobencha | v****n@r****g | 2 |
| Marc Carlson | m****n@f****g | 1 |
| Mattias | m****6@p****m | 1 |
| Hervé Pagès | h****b@g****m | 1 |
| LiNk-NY | m****9@g****m | 1 |
| m.carlson | m****n@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 56
- Total pull requests: 12
- Average time to close issues: about 1 year
- Average time to close pull requests: about 2 months
- Total issue authors: 35
- Total pull request authors: 5
- Average comments per issue: 2.32
- Average comments per pull request: 1.67
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Issue authors: 3
- 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
- lpantano (17)
- drives28 (4)
- elcega (3)
- sandray-imp (1)
- CroixJeremy2 (1)
- ShaowenJ (1)
- bacas2 (1)
- jgarces02 (1)
- etbuface (1)
- wangmhan (1)
- RubenRBakker (1)
- kesner (1)
- sum732 (1)
- fatemehkordevani (1)
- lgallegovillar (1)
Pull Request Authors
- roryk (4)
- vbarrera (4)
- zellerivo (3)
- idelvall (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 75,972 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 9
- Total maintainers: 1
bioconductor.org: DEGreport
Report of DEG analysis
- Homepage: http://lpantano.github.io/DEGreport/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/DEGreport/inst/doc/DEGreport.pdf
- License: MIT + file LICENSE
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Latest release: 1.44.0
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- Biobase * imports
- BiocGenerics * imports
- ComplexHeatmap * imports
- ConsensusClusterPlus * imports
- DESeq2 * imports
- RColorBrewer * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- broom * imports
- circlize * imports
- cluster * imports
- cowplot * imports
- dplyr * imports
- edgeR * imports
- ggdendro * imports
- ggplot2 * imports
- ggrepel * imports
- grDevices * imports
- grid * imports
- knitr * imports
- lasso2 * imports
- logging * imports
- magrittr * imports
- methods * imports
- psych * imports
- reshape * imports
- rlang * imports
- scales * imports
- stats * imports
- stringr * imports
- tibble * imports
- tidyr * imports
- utils * imports
- AnnotationDbi * suggests
- BiocStyle * suggests
- limma * suggests
- pheatmap * suggests
- rmarkdown * suggests
- statmod * suggests
- testthat * suggests
- python latest build