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scfa

A tool for cancer subtyping and risk score prediction using multi-omics data.

https://github.com/duct317/scfa

Science Score: 33.0%

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
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: frontiersin.org
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics sequencing transcriptomics ontology grna-sequence immune-repertoire proteomics
Last synced: 11 months ago · JSON representation

Repository

A tool for cancer subtyping and risk score prediction using multi-omics data.

Basic Info
  • Host: GitHub
  • Owner: duct317
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1.05 MB
Statistics
  • Stars: 3
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 6 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

SCFA

Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in order to reliably identify cancer subtypes and accurately predict risk scores of patients.

How to install

  • The package can be installed from this repository.
  • Install devtools: utils::install.packages('devtools')
  • Install the package using: devtools::install_github('duct317/SCFA')
  • When the package is loaded, it will check for the necessary libtorch: library(SCFA)
    libtorch can be installed using: torch::install_torch() # Example Please follow the vignette to run the package on example data. # Citation: Tran, D., Nguyen, H., Le, U., Bebis, G., Luu, H. N., & Nguyen, T. (2020). A Novel Method for Cancer Subtyping and Risk Prediction Using Consensus Factor Analysis, Frontiers in Oncology, 10, 1052. (link)

Owner

  • Name: Duc Tran
  • Login: duct317
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 55
  • Total Committers: 3
  • Avg Commits per committer: 18.333
  • Development Distribution Score (DDS): 0.182
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
duct317 d****t@n****u 45
Nitesh Turaga n****a@g****m 8
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 nevada.unr.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • 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
Pull Request Authors
  • duct317 (2)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • BiocParallel * imports
  • Matrix * imports
  • RhpcBLASctl * imports
  • cluster * imports
  • clusterCrit * imports
  • coro * imports
  • glmnet * imports
  • igraph * imports
  • matrixStats * imports
  • methods * imports
  • psych * imports
  • stats * imports
  • survival * imports
  • torch >= 0.3.0 imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests