censcyt
This is the released version of censcyt; for the devel version, see censcyt.
Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Bioconductor version: Release (3.23)
Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.
Author: Reto Gerber [aut, cre]
Maintainer: Reto Gerber <gerberreto at pm.me>
citation("censcyt")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("censcyt")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("censcyt")| Censored covariate | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software, Survival |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0), diffcyt |
| Imports | BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils |
| System Requirements | |
| URL | https://github.com/retogerber/censcyt |
| Bug Reports | https://github.com/retogerber/censcyt/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | censcyt_1.20.0.tar.gz |
| Windows Binary (x86_64) | censcyt_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | censcyt_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | censcyt_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/censcyt |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/censcyt |
| Bioc Package Browser | https://code.bioconductor.org/browse/censcyt/ |
| Package Short Url | https://bioconductor.org/packages/censcyt/ |
| Package Downloads Report | Download Stats |