RAIDS

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Science Score: 39.0%

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DOI references
Found 4 DOI reference(s) in README
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Low similarity (12.5%) to scientific vocabulary

Keywords

ancestry cancer-genomics exome-sequencing genomics inference r-language r-package rna-seq rna-sequencing whole-genome-sequencing

Last synced: 6 months ago · JSON representation

Repository

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Basic Info

Host: GitHub
Owner: KrasnitzLab
License: other
Language: R
Default Branch: main
Homepage: https://krasnitzlab.github.io/RAIDS/
Size: 9.37 MB

Statistics

Stars: 5
Watchers: 2
Forks: 4
Open Issues: 0
Releases: 10

Topics

ancestry cancer-genomics exome-sequencing genomics inference r-language r-package rna-seq rna-sequencing whole-genome-sequencing

Created almost 4 years ago · Last pushed 9 months ago

Metadata Files

Readme License

Robust genetic ancestry inference from challenging molecular data with RAIDS

The Robust Ancestry Inference using Data Synthesis (RAIDS) package enables accurate and robust inference of genetic ancestry from various types of molecular data, including whole-genome, whole-exome, targeted gene panels and RNA sequences, as described in our manuscript. Our tools retain high accuracy in presence of somatic alterations, such as those caused by cancer.

This code and analysis pipeline were designed and developed for the following publication:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

Authors

Pascal Belleau, Astrid Deschênes, David A. Tuveson and Alexander Krasnitz

Citing

If you use the RAIDS package for a publication, we would ask you to cite the following:

Pascal Belleau, Astrid Deschênes, Nyasha Chambwe, David A. Tuveson, Alexander Krasnitz; Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58. https://doi.org/10.1158/0008-5472.CAN-22-0682

Bioconductor Package

The RAIDS package is now an official package of Bioconductor.

The current Bioconductor release can be directly downloaded from their website: Current release

Installation

To install this package from Bioconductor, start R (version "4.3" or later) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RAIDS")

To install the latest version accessible from Github, the devtools package is required.

 ## Load required package
 library(devtools)

 ## Install the latest version of RAIDS
 devtools::install_github('KrasnitzLab/RAIDS')

Documentation

RAIDS Website

RAIDS Get Started

License

This package and the underlying RAIDS code are distributed under the Apache-2.0 license. You are free to use and redistribute this software.

For more information on Apache-2.0 License see https://opensource.org/licenses/Apache-2.0

Maintainer

Pascal Belleau

Bugs/Feature requests

Please contact us for bug fixes or with feature requests.

Thanks!

Owner

Name: KrasnitzLab
Login: KrasnitzLab
Kind: organization

Repositories: 5
Profile: https://github.com/KrasnitzLab

GitHub Events

Total

Issues event: 2
Issue comment event: 4
Push event: 112
Pull request event: 106
Create event: 1

Last Year

Issues event: 2
Issue comment event: 4
Push event: 112
Pull request event: 106
Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 4
Total pull requests: 162
Average time to close issues: over 1 year
Average time to close pull requests: about 1 hour
Total issue authors: 2
Total pull request authors: 2
Average comments per issue: 4.5
Average comments per pull request: 0.2
Merged pull requests: 159
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 63
Average time to close issues: N/A
Average time to close pull requests: about 1 hour
Issue authors: 0
Pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 0.05
Merged pull requests: 60
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

adeschen (2)
mdozmorov (2)
belleau (1)

Pull Request Authors

adeschen (175)
belleau (42)

Top Labels

Issue Labels

enhancement (2)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 4,399 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

bioconductor.org: RAIDS

Robust Ancestry Inference using Data Synthesis

Homepage: https://krasnitzlab.github.io/RAIDS/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/RAIDS/inst/doc/RAIDS.pdf
License: Apache License (>= 2)
Latest release: 1.6.1
published 10 months ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 4,399 Total

Rankings

Dependent repos count: 0.0%

Forks count: 12.4%

Stargazers count: 19.6%

Dependent packages count: 31.7%

Average: 32.4%

Downloads: 98.3%

Maintainers (1)

pascal_belleau@hotmail.com