transcriptogramer
This is the development version of transcriptogramer; for the stable release version, see transcriptogramer.
Transcriptional analysis based on transcriptograms
Bioconductor version: Development (3.21)
R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.
Author: Diego Morais [aut, cre], Rodrigo Dalmolin [aut]
Maintainer: Diego Morais <vinx at ufrn.edu.br>
citation("transcriptogramer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("transcriptogramer")
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("transcriptogramer")| The transcriptogramer user's guide | HTML | R Script |
| Reference Manual |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, RNASeq, Software, SystemsBiology, Transcription, Visualization |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.4), methods |
| Imports | biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO |
| System Requirements | Java Runtime Environment (>= 6) |
| URL | https://github.com/arthurvinx/transcriptogramer |
| Bug Reports | https://github.com/arthurvinx/transcriptogramer/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics |
| 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 | transcriptogramer_1.29.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/transcriptogramer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/transcriptogramer |
| Bioc Package Browser | https://code.bioconductor.org/browse/transcriptogramer/ |
| Package Short Url | https://bioconductor.org/packages/transcriptogramer/ |
| Package Downloads Report | Download Stats |