transcriptogramer

DOI: 10.18129/B9.bioc.transcriptogramer    

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

Transcriptional analysis based on transcriptograms

Bioconductor version: Development (3.8)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("transcriptogramer")

Documentation

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

Details

biocViews Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, RNASeq, Software, SystemsBiology, Transcription, Visualization
Version 1.3.2
License GPL (>= 2)
Depends R (>= 3.4), methods
Imports biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, 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
Build Report  

Package Archives

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

Source Package transcriptogramer_1.3.2.tar.gz
Windows Binary transcriptogramer_1.3.2.zip
Mac OS X 10.11 (El Capitan) transcriptogramer_1.3.2.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 http://bioconductor.org/packages/transcriptogramer/
Package Downloads Report Download Stats

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