mitch - Multi-Contrast Gene Set Enrichment Analysis
mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA concept dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is useful for pathway analysis of profiling studies with one, two or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. mitch is perfectly suited for pathway level differential analysis of scRNA-seq data. We have an established routine for pathway enrichment of Infinium Methylation Array data (see vignette). The main strengths of mitch are that it can import datasets easily from many upstream tools and has advanced plotting features to visualise these enrichments.
Last updated 9 days ago
geneexpressiongenesetenrichmentsinglecelltranscriptomicsepigeneticsproteomicsdifferentialexpressionreactomednamethylationmethylationarraygene-regulationgene-seq-analysispathway-analysis
5.86 score 16 stars 15 scripts 154 downloadsgetDEE2 - Programmatic access to the DEE2 RNA expression dataset
Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).
Last updated 24 days ago
geneexpressiontranscriptomicssequencingbioinformaticsdata-mininggenomicsrna-expressionrna-seq
3.90 score 4 stars 5 scripts 132 downloads