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censcyt

Censored predictors in differential abundance analysis

https://github.com/retogerber/censcyt

Science Score: 23.0%

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
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary

Keywords from Contributors

bioconductor-package
Last synced: 9 months ago · JSON representation

Repository

Censored predictors in differential abundance analysis

Basic Info
  • Host: GitHub
  • Owner: retogerber
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 168 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

censcyt

Bioc devel Bioc release R build status codecov

Summary

censcyt is an R package extending the diffcyt (differential discovery in high-dimensional cytometry via high-resolution clustering) pipeline. censcyt (Censored diffcyt) includes methods for differential abundance analysis in the presence of a covariate subject to right censoring. It uses the reversed association testing approach (like diffcyt) meaning the censored variable (e.g. survival time) is modeled as a predictor. Classical survival analysis methods on the other hand model the censored variable as the response. See also here.

Vignettes

The main workflow can be found in the Bioconductor package vignette of diffcyt. An example use of the censcyt methods for differential abundance analysis with a covariate subject to right censoring is available in the package vignette on bioconductor.

Install

To install from bioconductor: ```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("censcyt") ```

Development version

To install directly from GitHub run the following code: ```{r}

First install 'devtools' package from CRAN

install.packages("devtools")

Then install 'censcyt' package from GitHub

devtools::install_github("retogerber/censcyt") ```

Owner

  • Login: retogerber
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 46
  • Total Committers: 5
  • Avg Commits per committer: 9.2
  • Development Distribution Score (DDS): 0.543
Past Year
  • Commits: 4
  • Committers: 2
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
retogerber r****b@g****m 21
retogerber 4****r 15
Nitesh Turaga n****a@g****m 6
Reto Gerber r****r@u****h 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 uzh.ch: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • 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: 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
Pull Request Authors
  • retogerber (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 7,173 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: censcyt

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 7,173 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 27.2%
Downloads: 81.5%
Maintainers (1)
gerberreto@pm.me
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • diffcyt * depends
  • BiocParallel * imports
  • MASS * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • broom.mixed * imports
  • dirmult * imports
  • dplyr * imports
  • edgeR * imports
  • fitdistrplus * imports
  • lme4 * imports
  • magrittr * imports
  • methods * imports
  • mice * imports
  • multcomp * imports
  • purrr * imports
  • rlang * imports
  • stats * imports
  • stringr * imports
  • survival * imports
  • tibble * imports
  • tidyr * imports
  • utils * imports
  • BiocStyle * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
.github/workflows/test-coverage.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite