smithery/gptomics

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bio-alignment-filtering Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific …

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bio-alignment-indexing Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignm…

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bio-alignment-io Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Sto…

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bio-alignment-msa-parsing Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyz…

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bio-alignment-msa-statistics Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarit…

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bio-alignment-pairwise Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, find…

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bio-alignment-sorting Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, …

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bio-alignment-validation Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other po…

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bio-atac-seq-atac-peak-calling Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC.

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bio-atac-seq-atac-qc ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC…

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bio-atac-seq-differential-accessibility Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR.

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bio-atac-seq-motif-deviation Analyze TF motif accessibility variability across samples or single cells using chromVAR.

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bio-atac-seq-nucleosome-positioning Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATAC…

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bio-bam-statistics Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing align…

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bio-batch-downloads Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic.

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bio-batch-processing Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk…

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bio-blast-searches Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequen…

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bio-chipseq-motif-analysis Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER,…

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bio-chipseq-peak-calling Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input con…

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bio-chipseq-qc Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library …

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bio-chipseq-super-enhancers Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCO…

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bio-chipseq-visualization Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenome…

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bio-clinical-databases-clinvar-lookup Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpreta…

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bio-clinical-databases-dbsnp-queries Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF represe…

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bio-clinical-databases-gnomad-frequencies Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, L…

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bio-clinical-databases-myvariant-queries Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations i…

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bio-clinical-databases-pharmacogenomics Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B…

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bio-clinical-databases-polygenic-risk Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, Bridge…

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bio-clinical-databases-somatic-signatures Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs us…

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bio-clinical-databases-tumor-mutational-burden Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, p…

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bio-clinical-databases-variant-prioritization Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous…

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bio-clip-seq-binding-site-annotation Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA,…

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bio-clip-seq-clip-alignment Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-pre…

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bio-clip-seq-clip-motif-analysis Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo…

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bio-clip-seq-clip-peak-calling Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Pa…

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bio-clip-seq-clip-preprocessing Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extracti…

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bio-codon-usage Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CA…

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bio-compressed-files Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools.

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bio-consensus-sequences Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/…

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bio-copy-number-cnv-annotation Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, pop…

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bio-copy-number-cnv-visualization Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACET…

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bio-copy-number-cnvkit-analysis Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a rea…

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bio-copy-number-gatk-cnv Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, Denoi…

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bio-crispr-screens-base-editing-analysis Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchm…

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bio-crispr-screens-crispresso-editing Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR),…

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bio-crispr-screens-hit-calling Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK…

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bio-crispr-screens-jacks-analysis Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA …

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bio-crispr-screens-library-design Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, b…

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bio-crispr-screens-screen-qc Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson an…

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bio-data-visualization-color-palettes Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency…

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