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RTCGA

Download, integration and visualizations of the variety & volume of TCGA data.

https://github.com/rtcga/rtcga

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 11 committers (18.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords from Contributors

interpretability
Last synced: 11 months ago · JSON representation

Repository

Download, integration and visualizations of the variety & volume of TCGA data.

Basic Info
Statistics
  • Stars: 51
  • Watchers: 6
  • Forks: 32
  • Open Issues: 3
  • Releases: 0
Created over 11 years ago · Last pushed almost 4 years ago
Metadata Files
Readme

README.md

Travis-CI Build Status Project Status: Inactive - The project has reached a stable, usable state but is not being actively developed.

The family of R packages containing TCGA data

Data packages not yet submitted to Bioconductor from 2016-01-28 release date of TCGA data.

Data packages submitted to Bioconductor from 2015-11-01 release date of TCGA data.

Installation of packages from the RTCGA family:

Windows users:

Make sure you have rtools installed on your computer.

```{R}

some packages might be still only available on the devel version of Bioconductor

BiocInstaller::useDevel() # swiches to devel branchof Bioconductor - don't use this line if you are interested in release versions source("https://bioconductor.org/biocLite.R") # downloads bioClite function ```

|package |installation |help |releaseDate | |:--------------------------|:----------------------------------------|:-----------------------|:------------| |RTCGA.rnaseq.20160128 |biocLite('RTCGA.rnaseq.20160128') |?rnaseq.20160128 |2016-01-28 | |RTCGA.clinical.20160128 |biocLite('RTCGA.clinical.20160128') |?clinical.20160128 |2016-01-28 | |RTCGA.mutations.20160128 |biocLite('RTCGA.mutations.20160128') |?mutations.20160128 |2016-01-28 | |RTCGA.mRNA.20160128 |biocLite('RTCGA.mRNA.20160128') |?mRNA.20160128 |2016-01-28 | |RTCGA.miRNASeq.20160128 |biocLite('RTCGA.miRNASeq.20160128') |?miRNASeq.20160128 |2016-01-28 | |RTCGA.RPPA.20160128 |biocLite('RTCGA.RPPA.20160128') |?RPPA.20160128 |2016-01-28 | |RTCGA.CNV.20160128 |biocLite('RTCGA.CNV.20160128') |?CNV.20160128 |2016-01-28 | |RTCGA.methylation.20160128 |biocLite('RTCGA.methylation.20160128') |?methylation.20160128 |2016-01-28 | |RTCGA.rnaseq |biocLite('RTCGA.rnaseq') |?rnaseq |2015-11-01 | |RTCGA.clinical |biocLite('RTCGA.clinical') |?clinical |2015-11-01 | |RTCGA.mutations |biocLite('RTCGA.mutations') |?mutations |2015-11-01 | |RTCGA.mRNA |biocLite('RTCGA.mRNA') |?mRNA |2015-11-01 | |RTCGA.miRNASeq |biocLite('RTCGA.miRNASeq') |?miRNASeq |2015-11-01 | |RTCGA.PANCAN12 |biocLite('RTCGA.PANCAN12') |?pancan12 |NULL | |RTCGA.RPPA |biocLite('RTCGA.RPPA') |?RPPA |2015-11-01 | |RTCGA.CNV |biocLite('RTCGA.CNV') |?CNV |2015-11-01 | |RTCGA.methylation |biocLite('RTCGA.methylation') |?methylation |2015-11-01 |

RTCGA

Packages from the RTCGA.data - family/factory are based on the RTCGA package

Installation of the RTCGA package:

To get started, install the latest version of RTCGA from Bioconductor:

{R} BiocInstaller::useDevel() # swiches to devel branch of Bioconductor source("https://bioconductor.org/biocLite.R") # downloads bioClite function biocLite("RTCGA") # installs a package or use below code to download the development version which is like to be less bugged than the release version on Bioconductor: {R} if (!require(devtools)) { install.packages("devtools") require(devtools) } install_github("RTCGA/RTCGA", build_vignettes = TRUE) To check Use Cases run {R} browseVignettes("RTCGA")

Authors:

Marcin Kosiński, m.p.kosinski@gmail.com

Przemysław Biecek, przemyslaw.biecek@gmail.com

Witold Chodor, witoldchodor@gmail.com

This repository is synchronized with it's Bioconductor's SVN devel mirror.

RTCGA logo

Owner

  • Name: RTCGA
  • Login: RTCGA
  • Kind: organization

A factory of R packages containing The Cancer Genome Atlas Project datasets.

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 342
  • Total Committers: 11
  • Avg Commits per committer: 31.091
  • Development Distribution Score (DDS): 0.456
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
MarcinKosinski k****m@s****l 186
Marcin Kosiński m****i@g****m 83
pbiecek p****k@g****m 35
m.kosinski m****i@b****8 11
witia1990 w****0@s****l 11
Quares k****i@g****m 5
Marcin Kosiński m****i@p****l 4
Alboukadel KASSAMBARA a****a@g****m 2
d.tenenbaum d****m@b****8 2
j.hester j****r@b****8 2
mkosinski M****i@g****l 1
Committer Domains (Top 20 + Academic)
grupawp.pl: 1 prodataconsult.pl: 1 students.mimuw.edu.pl: 1 student.mini.pw.edu.pl: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 99
  • Total pull requests: 1
  • Average time to close issues: 2 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 21
  • Total pull request authors: 1
  • Average comments per issue: 2.08
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MarcinKosinski (67)
  • pbiecek (5)
  • DecodeGenome (4)
  • wchodor (3)
  • DarioS (2)
  • cqneosun (2)
  • hsiowa2 (1)
  • zyb1984 (1)
  • atakanekiz (1)
  • kieranrcampbell (1)
  • shaneahmed (1)
  • seedson (1)
  • vobencha (1)
  • ghost (1)
  • JuliaArizanova (1)
Pull Request Authors
  • kassambara (1)
Top Labels
Issue Labels
marketing (10) functionality (6) enhancement (5) help wanted (2) proposition (2) wontfix (2) management (2) TODO (2) invalid (1) question (1) duplicate (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 84,234 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: RTCGA

The Cancer Genome Atlas Data Integration

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 84,234 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 4.0%
Downloads: 11.9%
Maintainers (1)
m.p.kosinski@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3.0 depends
  • XML * imports
  • assertthat * imports
  • data.table * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggthemes * imports
  • htmltools * imports
  • knitr * imports
  • purrr * imports
  • rmarkdown * imports
  • rvest * imports
  • scales * imports
  • stringi * imports
  • survival * imports
  • survminer * imports
  • viridis * imports
  • xml2 * imports
  • Biobase * suggests
  • GenomicRanges * suggests
  • IRanges * suggests
  • RTCGA.CNV * suggests
  • RTCGA.CNV.20160128 * suggests
  • RTCGA.PANCAN12 * suggests
  • RTCGA.RPPA * suggests
  • RTCGA.RPPA.20160128 * suggests
  • RTCGA.clinical * suggests
  • RTCGA.clinical.20160128 * suggests
  • RTCGA.mRNA * suggests
  • RTCGA.mRNA.20160128 * suggests
  • RTCGA.methylation * suggests
  • RTCGA.methylation.20160128 * suggests
  • RTCGA.miRNASeq * suggests
  • RTCGA.miRNASeq.20160128 * suggests
  • RTCGA.mutations * suggests
  • RTCGA.mutations.20160128 * suggests
  • RTCGA.rnaseq * suggests
  • RTCGA.rnaseq.20160128 * suggests
  • S4Vectors * suggests
  • devtools * suggests
  • magrittr * suggests
  • pander * suggests
  • testthat * suggests
  • tidyr * suggests
devel/RTCGA.tools/DESCRIPTION cran
  • R >= 3.2.0 depends
  • RTCGA * depends
  • RTCGA.PANCAN12 * suggests
  • RTCGA.clinical * suggests
  • RTCGA.cnv * suggests
  • RTCGA.mutations * suggests
  • RTCGA.rnaseq * suggests