r-bioc-dexseq
GNU R inference of differential exon usage in RNA-Seq
The package is focused on finding differential exon usage
using RNA-seq exon counts between samples with different
experimental designs. It provides functions that allows the
user to make the necessary statistical tests based on a model
that uses the negative binomial distribution to estimate the
variance between biological replicates and generalized linear
models for testing. The package also provides functions for the
visualization and exploration of the results.
r-bioc-htsfilter
GNU R filter replicated high-throughput transcriptome sequencing data
This package implements a filtering procedure for
replicated transcriptome sequencing data based on a global
Jaccard similarity index in order to identify genes with low,
constant levels of expression across one or more experimental
conditions.
r-bioc-genomicfeatures
GNU R tools for making and manipulating transcript centric annotations
A set of tools and methods for making and manipulating transcript
centric annotations. With these tools the user can easily download the
genomic locations of the transcripts, exons and cds of a given organism,
from either the UCSC Genome Browser or a BioMart database (more sources
will be supported in the future). This information is then stored in a
local database that keeps track of the relationship between transcripts,
exons, cds and genes. Flexible methods are provided for extracting the
desired features in a convenient format.
r-bioc-go.db
annotation maps describing the entire Gene Ontology
This package is part of BioConductor and provides a set of annotation
maps describing the entire Gene Ontology assembled using data from GO.
r-bioc-gosemsim
GO-terms semantic similarity measures
The semantic comparisons of Gene Ontology (GO) annotations provide
quantitative ways to compute similarities between genes and gene groups,
and have became important basis for many bioinformatics analysis approaches.
GOSemSim is an R package for semantic similarity computation among GO terms,
sets of GO terms, gene products and gene clusters. GOSemSim implemented five
methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
r-bioc-netsam
Network Seriation And Modularization
The NetSAM (Network Seriation and Modularization) package
takes an edge-list representation of a network as an input,
performs network seriation and modularization analysis, and
generates as files that can be used as an input for the
one-dimensional network visualization tool NetGestalt
(http://www.netgestalt.org) or other network analysis.