VISTA - Visualization and Integrated System for Transcriptomic Analysis
VISTA (Visualization and Integrated System for Transcriptomic Analysis) runs bulk RNA-seq differential expression with DESeq2, edgeR or limma-voom, or a DESeq2/edgeR consensus, and keeps counts, results for every contrast, gene annotation, colours and analysis parameters in one validated SummarizedExperiment-derived object. Plotting functions, GO, KEGG and MSigDB enrichment, optional cell-type deconvolution and a Quarto report all read that object, and an exported benchmark checks its results against independent DESeq2, edgeR and limma runs.
Last updated
rnaseqdifferentialexpressiongeneexpressiontranscriptomicsvisualization
6.34 score 10 stars 34 scripts 438 downloads
BamScale - Bioconductor-Friendly Multithreaded BAM Processing
Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScale provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.
Last updated
softwaredataimportsequencingcoveragealignmentqualitycontrolzlibcppopenmp
5.00 score 502 downloadsfastRanges - Deterministic Multithreaded Genomic Interval Operations
High-performance interval overlap and join operations for 'IRanges' and 'GenomicRanges'. The package provides deterministic multithreaded overlap computation, reusable subject indexes for repeated queries, and join helpers that keep range metadata in a consistent output grammar.
Last updated
softwareinfrastructuresequencingcpp
4.78 score 3 stars 5 scripts 338 downloads
BamScaleR - Bioconductor-Friendly Multithreaded BAM Processing
Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScaleR provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.
Last updated
softwaredataimportsequencingcoveragealignmentqualitycontrolzlibcppopenmp
4.08 score