Science Score: 59.0%
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
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: scholar.google -
✓Committers with academic emails
2 of 37 committers (5.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
TCGAbiolinks
Basic Info
- Host: GitHub
- Owner: BioinformaticsFMRP
- Language: R
- Default Branch: master
- Homepage: http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
- Size: 349 MB
Statistics
- Stars: 331
- Watchers: 23
- Forks: 120
- Open Issues: 268
- Releases: 0
Topics
Metadata Files
README.md
TCGAbiolinks - An R/Bioconductor package for integrative analysis with TCGA data
TCGAbiolinks is able to access The National Cancer Institute (NCI) Genomic Data Commons (GDC) thorough its GDC Application Programming Interface (API) to search, download and prepare relevant data for analysis in R.
Installation from GitHub
```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") ```
Installation from Bioconductor
```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("TCGAbiolinks") ```
Docker image
TCGAbiolinks is available as Docker image (self-contained environments that contain everything needed to run the software), which can be easily run on Mac OS, Windows and Linux systems.
This PDF show how to install and execute the image.
The image can be obtained from Docker Hub: https://hub.docker.com/r/tiagochst/tcgabiolinksgui/
For more information please check: https://docs.docker.com/ and https://www.bioconductor.org/help/docker/
Manual
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
Citation
Please cite both TCGAbiolinks package:
Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.
Mounir, Mohamed, Lucchetta, Marta, Silva, C T, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena (2019). “New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.” PLoS computational biology, 15(3), e1006701.
Silva TC, Colaprico A, Olsen C et al.TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]. F1000Research 2016, 5:1542 (https://doi.org/10.12688/f1000research.8923.2)
Also, if you have used ELMER analysis please cite:
- Yao, L., Shen, H., Laird, P. W., Farnham, P. J., & Berman, B. P. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome Biol 16 (2015): 105.
- Yao, Lijing, Benjamin P. Berman, and Peggy J. Farnham. "Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes." Critical reviews in biochemistry and molecular biology 50.6 (2015): 550-573.
- Tiago C Silva, Simon G Coetzee, Nicole Gull, Lijing Yao, Dennis J Hazelett, Houtan Noushmehr, De-Chen Lin, Benjamin P Berman, ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles, Bioinformatics, Volume 35, Issue 11, 1 June 2019, Pages 1974–1977, https://doi.org/10.1093/bioinformatics/bty902
Owner
- Name: OMICs Bioinformatics Tools
- Login: BioinformaticsFMRP
- Kind: organization
- Repositories: 12
- Profile: https://github.com/BioinformaticsFMRP
GitHub Events
Total
- Issues event: 14
- Watch event: 29
- Issue comment event: 51
- Push event: 10
- Pull request event: 3
- Fork event: 10
Last Year
- Issues event: 14
- Watch event: 29
- Issue comment event: 51
- Push event: 10
- Pull request event: 3
- Fork event: 10
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| tiagochst | t****t@g****m | 19,427 |
| Tiago Chedraoui Silva | t****m | 3,350 |
| torongs82 | a****o@g****m | 2,721 |
| Simo Mounir | m****2@g****m | 222 |
| torongs82 | a****o@A****l | 70 |
| torongs82 | a****o@a****e | 70 |
| torongs82 | a****o@a****k | 70 |
| colsen | c****n@u****e | 64 |
| Melkiades | d****i@g****m | 62 |
| Mohamed Mounir | s****r@M****l | 54 |
| vobencha | v****n@r****g | 54 |
| vobencha | v****a@g****m | 54 |
| Nitesh Turaga | n****a@g****m | 48 |
| a.colaprico | a****o@b****8 | 44 |
| Tiago Silva | t****a@T****l | 42 |
| Dan Tenenbaum | d****a@f****g | 36 |
| lucgar | l****8@g****m | 36 |
| Yohann | y****c@g****m | 27 |
| LiNk-NY | m****9@g****m | 27 |
| Xu Ren | x****n@s****u | 27 |
| Antonio Colaprico | a****o@u****e | 26 |
| Hervé Pagès | h****s@f****g | 24 |
| Herve Pages | h****s@f****g | 24 |
| Dario Romagnoli | d****7@g****m | 22 |
| Tiago Silva | t****a@T****t | 13 |
| Gioele Ciaparrone | J****3 | 12 |
| t.silva | t****a@b****8 | 11 |
| J Wokaty | j****y@s****u | 10 |
| Tiago Silva | t****a@e****m | 8 |
| Tiago Maié | t****e@h****m | 8 |
| and 7 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 112
- Total pull requests: 5
- Average time to close issues: 3 months
- Average time to close pull requests: 3 months
- Total issue authors: 86
- Total pull request authors: 5
- Average comments per issue: 3.36
- Average comments per pull request: 1.2
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 12
- Pull requests: 1
- Average time to close issues: about 16 hours
- Average time to close pull requests: 4 days
- Issue authors: 12
- Pull request authors: 1
- Average comments per issue: 0.08
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cloudred20 (3)
- bigwiz83 (3)
- xiatingp (3)
- DarioS (3)
- needleworm (3)
- AndreVidas (3)
- cstubben (3)
- chen1111111 (3)
- Melkiades (2)
- SonicHedgehogSHH (2)
- hongenxu (2)
- mattiasaine (2)
- RunDevilRun (2)
- IvanEllson (2)
- kvougas (2)
Pull Request Authors
- Juggernaut93 (1)
- NolanBentley (1)
- Melkiades (1)
- warbol (1)
- MarcinKosinski (1)
- Lancelof2019 (1)
- fabianjkrueger (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 489,148 total
- Total dependent packages: 7
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 2
bioconductor.org: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
- Homepage: https://github.com/BioinformaticsFMRP/TCGAbiolinks
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/TCGAbiolinks.pdf
- License: GPL (>= 3)
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Latest release: 2.36.0
published 10 months ago
Rankings
Maintainers (2)
Dependencies
- R >= 4.0 depends
- GenomicRanges * imports
- IRanges * imports
- R.utils * imports
- S4Vectors * imports
- SummarizedExperiment >= 1.4.0 imports
- TCGAbiolinksGUI.data imports
- XML >= 3.98.0 imports
- biomaRt * imports
- data.table * imports
- downloader >= 0.4 imports
- dplyr * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- httr >= 1.2.1 imports
- jsonlite >= 1.0.0 imports
- knitr * imports
- methods * imports
- plyr * imports
- purrr * imports
- readr * imports
- rvest >= 0.3.0 imports
- stats * imports
- stringr >= 1.0.0 imports
- tibble * imports
- tidyr * imports
- tools * imports
- utils * imports
- xml2 * imports
- AnnotationHub * suggests
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