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transcriptogramer

This is the development version of transcriptogramer; for the stable release version, see transcriptogramer.

Transcriptional analysis based on transcriptograms


Bioconductor version: Development (3.19)

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 (from within R, enter citation("transcriptogramer")):

Installation

To install this package, start R (version "4.4") 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 PDF
NEWS Text

Details

biocViews Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, RNASeq, Software, SystemsBiology, Transcription, Visualization
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package transcriptogramer_1.25.0.tar.gz
Windows Binary transcriptogramer_1.25.0.zip
macOS Binary (x86_64) transcriptogramer_1.25.0.tgz
macOS Binary (arm64) transcriptogramer_1.25.0.tgz
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