GSVA - Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Last updated 2 days ago

functionalgenomicsmicroarrayrnaseqpathwaysgenesetenrichmentgene-set-enrichmentgenomicspathway-enrichment-analysis

187 stars 7.66 score 93 dependencies 18 dependents

GenomicScores - Infrastructure to work with genomewide position-specific scores

Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

Last updated 4 months ago

infrastructuregeneticsannotationsequencingcoverageannotationhubsoftware

8 stars 2.89 score 73 dependencies 6 dependents

qpgraph - Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Last updated 4 months ago

microarraygeneexpressiontranscriptionpathwaysnetworkinferencegraphandnetworkgeneregulationgeneticsgeneticvariabilitysnpsoftware

2.73 score 74 dependencies 2 dependents

gDNAx - Diagnostics for assessing genomic DNA contamination in RNA-seq data

Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.

Last updated 27 days ago

transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomicssplicedalignmentalignment

1.69 score 93 dependencies

VariantFiltering - Filtering of coding and non-coding genetic variants

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Last updated 4 months ago

geneticshomo_sapiensannotationsnpsequencinghighthroughputsequencing

4 stars 1.64 score 169 dependencies

atena - Analysis of Transposable Elements

Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.

Last updated 4 months ago

transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomics

7 stars 1.51 score 91 dependencies