featurecounts-rna-counting
De la autor
Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.
Instalare
npx skills add jaechang-hits/SciAgent-Skills --skill featurecounts-rna-counting -a claude-code
Se instalează în .claude/skills/featurecounts-rna-counting/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Fără descărcare: licența acestui skill (GPL-3.0) nu ne permite să-i redistribuim fișierele. Comenzile de instalare le iau direct de pe GitHub.
Vrei ca agentul să-ți propună skill-uri în timp ce scrii? Vezi cum folosești skill-urile din IDE.
Verificări de siguranță pe SKILL.md
- Folosește sudoScăzut
De ce 82
aiqbench calculează scorul de încredere din semnale publice. Nu este un audit de securitate, așa că citește un skill înainte să-l instalezi.
Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- bulk-rnaseqK-Dense-AI/scientific-agent-skillsPrepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification, or building a counts matrix for DESeq2. For single-cell data use scanpy; for statistical fitting alone use pydeseq2.Știință★ 54.1K
- star-rna-seq-alignerjaechang-hits/SciAgent-SkillsSplice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed for variant calling, IGV, or ENCODE pipelines.Știință★ 382
- salmon-rna-quantificationjaechang-hits/SciAgent-SkillsUltra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.Știință★ 382
- pysam-genomic-filesjaechang-hits/SciAgent-SkillsRead/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.Știință★ 382
- genomic-coordinatesK-Dense-AI/scientific-agent-skillsConverts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".Știință★ 54.1K
- pysamK-Dense-AI/scientific-agent-skillsProvides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.Știință★ 54.1K
Note și recenzii
—
nicio recenzie
Ai încercat acest skill? Notează-l ca să-i ajuți pe alții. Autentifică-te
Discuție
Intră în discuție. Autentifică-te