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Use when working with TxDb.Hsapiens.UCSC.hg38.knownGene, the Bioconductor annotation package providing UCSC hg38 transcript/gene coordinates for Homo sapiens. Handles transcript extraction, exon group
Use with AI
Install the MCP server or CLI to instantly fetch TxDb.Hsapiens.UCSC.hg38.knownGene documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/txdbhsapiensucschg38knowngene
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2 shared topics • 1 shared operation
BRAKER — fully automated gene structure annotation pipeline combining GeneMark-ES/ET/EP/ETP with AUGUSTUS training. Supports RNA-Seq evidence (BRAKER1), protein evidence (BRAKER2), and combined RNA-Se
2 shared topics • 1 shared operation
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 • 1 shared operation
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 • 1 shared operation
STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv
2 shared topics • 1 shared operation