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tximeta — R/Bioconductor package for importing transcript-level quantification data from Salmon, alevin, piscem, and other quantifiers with automatic metadata attachment. Automatically identifies the
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Install the MCP server or CLI to instantly fetch tximeta documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/tximeta
DRIMSeq is a Bioconductor R package for Differential Transcript Usage (DTU) analysis using a Dirichlet-multinomial distribution to model transcript-level count proportions. Tests whether relative tran
2 shared topics • 2 shared operations
gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr
2 shared topics • 2 shared operations
IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,
2 shared topics • 2 shared operations
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
2 shared topics • 2 shared operations
Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch
2 shared topics • 2 shared operations