TSENAT
This is the development version of TSENAT; to use it, please install the devel version of Bioconductor.
Tsallis Entropy Analysis Toolbox
Bioconductor version: Development (3.24)
Quantifies and models isoform-usage complexity in RNA-seq data using Tsallis entropy, a scale-dependent diversity measure. By tuning the entropic index parameter (q), TSENAT examines transcriptome heterogeneity at different scales: rare variants (low q) or dominant isoforms (high q). It enables computing Tsallis entropy and Tsallis divergence from transcript-level estimates, comparing measures between conditions, testing for differences, and visualizing scale-dependent complexity via q-curves.
Author: Cristóbal Gallardo Alba [aut, cre]
Maintainer: Cristóbal Gallardo Alba <gallardoalba at pm.me>
citation("TSENAT")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("TSENAT")
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("TSENAT")| 1. TSENAT: Tsallis Entropy Analysis Toolbox | HTML | R Script |
| 2. TSENAT Appendix A: Equivalence Validation | HTML | R Script |
| 3. TSENAT Appendix B: Cross-Method Validation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, TranscriptomeVariant, Transcriptomics |
| Version | 0.99.34 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | SummarizedExperiment, methods, stats, ggplot2, withr, BiocParallel, matrixStats, mgcv, geepack, pheatmap, cowplot, dplyr, tidyr, S4Vectors, rlang, Rcpp, memoise, digest, readr, ARTool |
| System Requirements | |
| URL | https://gallardoalba.github.io/TSENAT |
| Bug Reports | https://github.com/gallardoalba/TSENAT/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle, kableExtra, patchwork, covr, RColorBrewer, gamsel, glmmTMB, glmnet, gridExtra, nlme, fdrtool, MASS, SplicingFactory, devtools, gtable |
| Linking To | Rcpp, RcppArmadillo |
| 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 | TSENAT_0.99.34.tar.gz |
| Windows Binary (x86_64) | TSENAT_0.99.34.zip |
| macOS Binary (big-sur-x86_64) | TSENAT_0.99.34.tgz |
| macOS Binary (sonoma-arm64) | TSENAT_0.99.34.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TSENAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TSENAT |
| Bioc Package Browser | https://code.bioconductor.org/browse/TSENAT/ |
| Package Short Url | https://bioconductor.org/packages/TSENAT/ |
| Package Downloads Report | Download Stats |