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 [aut, cre]
Maintainer: Cristóbal Gallardo <gallardoalba at pm.me>
citation("TSENAT")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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: Non-Parametric Validation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, TranscriptomeVariant, Transcriptomics |
| Version | 0.99.17 |
| 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 |
| 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, microbenchmark, gtable, e1071 |
| 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_0.99.17.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | TSENAT_0.99.17.tgz |
| macOS Binary (sonoma-arm64) | |
| 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 |