transcriptogramer

DOI: 10.18129/B9.bioc.transcriptogramer    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see transcriptogramer.

Transcriptional analysis based on transcriptograms

Bioconductor version: 3.12

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 expression are altered.

Author: Diego Morais [aut, cre], Rodrigo Dalmolin [aut]

Maintainer: Diego Morais <vinx at ufrn.edu.br>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	The transcriptogramer user's guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, RNASeq, Software, SystemsBiology, Transcription, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.6 (R-3.4) (3.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
SystemRequirements	Java Runtime Environment (>= 6)
Enhances
URL	https://github.com/arthurvinx/transcriptogramer
BugReports	https://github.com/arthurvinx/transcriptogramer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	transcriptogramer_1.12.0.tar.gz
Windows Binary	transcriptogramer_1.12.0.zip
macOS 10.13 (High Sierra)	transcriptogramer_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/transcriptogramer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/transcriptogramer
Package Short Url	https://bioconductor.org/packages/transcriptogramer/
Package Downloads Report	Download Stats