fCI
This is the released version of fCI; for the devel version, see fCI.
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
DOI: 10.18129/B9.bioc.fCI
Bioconductor version: Release (3.23)
(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.
Author: Shaojun Tang
Maintainer: Shaojun Tang <tangshao2008 at gmail.com>
citation("fCI")):
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("fCI")
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("fCI")| fCI | HTML | R Script |
| Reference Manual |
Details
| biocViews | Proteomics, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.1), FNN, psych, gtools, zoo, rgl, grid, VennDiagram |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| 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 | fCI_1.42.0.tar.gz |
| Windows Binary (x86_64) | fCI_1.42.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | fCI_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | fCI_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fCI |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fCI |
| Bioc Package Browser | https://code.bioconductor.org/browse/fCI/ |
| Package Short Url | https://bioconductor.org/packages/fCI/ |
| Package Downloads Report | Download Stats |