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Sailfish — rapid mapping-based isoform quantification from RNA-seq reads. Uses quasi-mapping to estimate transcript abundance without full alignment. Provides TPM and estimated counts per transcript.
Use with AI
Install the MCP server or CLI to instantly fetch Sailfish documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/sailfish
FLAIR — Full-Length Alternative Isoform analysis of RNA for long-read sequencing. Corrects, defines, and quantifies transcript isoforms from nanopore cDNA, native RNA, and PacBio reads. Provides splic
2 shared topics • 2 shared operations
Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.
2 shared topics • 2 shared operations
SortMeRNA — fast filtering of ribosomal RNA reads from metatranscriptomic and RNA-seq data using local sequence alignment against curated rRNA databases (SILVA, RFAM). CLI tool for rRNA removal, rRNA
2 shared topics • 2 shared operations
CytoTRACE -- computational method for predicting relative differentiation state of cells from single-cell RNA-seq data. Uses gene counts (number of detectably expressed genes per cell) as a robust pro
2 shared topics • 1 shared operation
DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel
2 shared topics • 1 shared operation