smithery/gptomics

1

bio-genome-intervals-gtf-gff-handling Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/e…

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bio-genome-intervals-proximity-operations Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - near…

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bio-geo-data Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when fi…

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bio-hi-c-analysis-compartment-analysis Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-…

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bio-hi-c-analysis-contact-pairs Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library wor…

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bio-hi-c-analysis-hic-data-io Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using …

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bio-hi-c-analysis-hic-differential Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompa…

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bio-hi-c-analysis-hic-visualization Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-…

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bio-hi-c-analysis-matrix-operations Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected…

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bio-hi-c-analysis-tad-detection Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulat…

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bio-imaging-mass-cytometry-cell-segmentation Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler…

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bio-imaging-mass-cytometry-data-preprocessing Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover …

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bio-imaging-mass-cytometry-interactive-annotation Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, coveri…

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bio-imaging-mass-cytometry-phenotyping Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-…

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bio-imaging-mass-cytometry-quality-metrics Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (…

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bio-imaging-mass-cytometry-spatial-analysis Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, coveri…

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bio-local-blast Build local BLAST databases and run searches using NCBI BLAST+ command-line tools.

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bio-long-read-sequencing-basecalling Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and ac…

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bio-long-read-sequencing-clair3-variants Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-st…

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bio-long-read-sequencing-isoseq-analysis Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and …

smithery/gptomics

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bio-long-read-sequencing-long-read-alignment Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-match…

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bio-long-read-sequencing-long-read-qc Assesses Oxford Nanopore and PacBio long-read quality with NanoPlot, cramino, NanoComp, pycoQC/toulligQC, and seqkit,…

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bio-long-read-sequencing-medaka-polishing Polishes Oxford Nanopore draft assemblies to higher consensus accuracy with medaka, a basecaller-model-specific neura…

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bio-long-read-sequencing-nanopore-methylation Calls DNA base modifications (5mC, 5hmC, 6mA, 4mC) directly from Oxford Nanopore and PacBio HiFi long reads encoded a…

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bio-long-read-sequencing-structural-variants Detects structural variants (deletions, insertions, inversions, duplications, translocations) from Oxford Nanopore an…

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bio-metabolomics-lipidomics Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware di…

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bio-metabolomics-metabolite-annotation Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-…

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bio-metabolomics-msdial-preprocessing Runs the MS-DIAL preprocessing workflow (peak picking, MS2Dec spectral deconvolution, alignment, gap-filling) and imp…

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bio-metabolomics-normalization-qc Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing v…

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bio-metabolomics-pathway-mapping Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA),…

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bio-metabolomics-statistical-analysis Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs u…

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bio-metabolomics-targeted-analysis Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution…

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bio-metabolomics-xcms-preprocessing Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, takin…

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bio-metagenomics-abundance Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositi…

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bio-metagenomics-amr-detection Profiles the antimicrobial-resistance gene content (resistome) of shotgun metagenomes - read-based quantification wit…

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bio-metagenomics-functional-profiling Profiles the functional potential of shotgun metagenomes with HUMAnN 3's tiered search (MetaPhlAn prescreen, Bowtie2 …

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bio-metagenomics-kraken Classifies shotgun metagenomic reads to taxa with Kraken2's minimizer/LCA matching against a chosen reference databas…

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bio-metagenomics-metaphlan Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie…

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bio-metagenomics-strain-tracking Resolves and compares bacterial strains below the species level from shotgun metagenomes with inStrain (popANI/conANI…

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bio-metagenomics-visualization Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest fig…

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bio-methylation-bismark-alignment Aligns bisulfite-converted (WGBS, RRBS, PBAT) and enzymatic (EM-seq) short reads to an in-silico C->T/G->A-converted …

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bio-methylation-calling Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismark_methylation_extractor (Bisma…

smithery/gptomics

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43

bio-methylation-dmr-detection Detects differentially methylated regions (DMRs) from short-read bisulfite (WGBS/RRBS), array, and long-read methylat…

smithery/gptomics

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44

bio-methylation-methylkit Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results sp…

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bio-microbiome-amplicon-processing Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removin…

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bio-microbiome-differential-abundance Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-a…

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bio-microbiome-diversity-analysis Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenne…

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bio-microbiome-functional-prediction Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic int…

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bio-microbiome-qiime2-workflow Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (Fe…

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bio-microbiome-taxonomy-assignment Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and prim…

smithery/gptomics

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