SkillHealthcare & Life Sciences
🏥 Clinical Variant Reporter
Classify germline variants from VCF/BCF files according to the ACMG/AMP 2015 28-criteria evidence framework and
◈OpenClaw
By ClawBioOriginal project
MIT · FreeView skill
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SkillData & Analytics
Pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
✳Claude Code>_Codex↗Cursor+2
By DicklesworthstoneOriginal project
MIT · FreeView skill
SkillData & Analytics
CLIP-seq Preprocessing
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak...
✳Claude Code>_Codex◈OpenClaw+1
By GPTomicsOriginal project
MIT · FreeView skill
SkillData & Analytics
Splicing-Specific Quality Control
Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio d...
✳Claude Code>_Codex◈OpenClaw+1
By GPTomicsOriginal project
MIT · FreeView skill
SkillData & Analytics
BAM Statistics
Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
✳Claude Code>_Codex◈OpenClaw+1
By GPTomicsOriginal project
MIT · FreeView skill
SkillData & Analytics
🧬 Variant Annotation
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
◈OpenClaw
By Toby ClarkOriginal project
MIT · FreeView skill
SkillData & Analytics
samtools — SAM/BAM/CRAM Alignment Toolkit
CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
◈OpenClaw
By jaechang-hitsOriginal project
MIT · FreeView skill
SkillData & Analytics
Alignment Sorting
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
✳Claude Code>_Codex↗Cursor+1
By David-Li0406Original project
Apache-2.0 · FreeView skill
SkillData & Analytics
🧬 LD 1000G Region Compute
Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant. Single client (on-demand region fetch from ...
◈OpenClaw
By ClawBioOriginal project
MIT · FreeView skill
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