BioTIP
This is the released version of BioTIP; for the devel version, see BioTIP.
BioTIP: An R package for characterization of Biological Tipping-Point
Bioconductor version: Release (3.23)
Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.
Author: Zhezhen Wang, Andrew Goldstein, Yuxi Sun, Biniam Feleke, Qier An, Antonio Feliciano, Xinan Yang
Maintainer: Felix Yu <felixy at uchicago.edu> and X Holly Yang <xyang2 at uchicago.edu>
citation("BioTIP")):
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("BioTIP")
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("BioTIP")| BioTIP- an R package for characterization of Biological Tipping-Point | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, RNASeq, Sequencing, Software, Transcription |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-2 |
| Depends | R (>= 3.6) |
| Imports | igraph, cluster, psych, stringr, GenomicRanges, MASS, scran, methods, stats, utils, grDevices, graphics, foreach, doParallel |
| System Requirements | |
| URL | https://github.com/xyang2uchicago/BioTIP |
See More
| Suggests | knitr, markdown, base, rmarkdown, 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 | BioTIP_1.26.0.tar.gz |
| Windows Binary (x86_64) | BioTIP_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | BioTIP_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | BioTIP_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BioTIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BioTIP |
| Bioc Package Browser | https://code.bioconductor.org/browse/BioTIP/ |
| Package Short Url | https://bioconductor.org/packages/BioTIP/ |
| Package Downloads Report | Download Stats |