Research & Science · By GPTomics

Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative tradeoff, SMETANA for…

GPTomics/bioSkills

Builds tissue-, cell-type-, and condition-specific metabolic models by integrating transcriptomic or proteomic data into a generic genome-scale model, using extraction algorithms (GIMME, iMAT…

GPTomics/bioSkills

Performs flux balance analysis (FBA), flux variability analysis (FVA), parsimonious FBA (pFBA), loopless FBA, flux sampling, and production envelopes on genome-scale metabolic models with COBRApy…

GPTomics/bioSkills

Performs in-silico single and double gene deletions, condition-dependent essentiality, and synthetic-lethality screens on genome-scale metabolic models with COBRApy, evaluating gene-protein-reaction…

GPTomics/bioSkills

Builds draft genome-scale metabolic models from an annotated genome using CarveMe (top-down carving of a BiGG universal model) or gapseq (bottom-up pathway-evidence reconstruction), then loads and…

GPTomics/bioSkills

Validates, gap-fills, and standardizes genome-scale metabolic models using memote for consistency and annotation scoring and COBRApy for manual curation, including mass/charge balance…

GPTomics/bioSkills

Computes metabolic-engineering strain designs on genome-scale models with StrainDesign (OptKnock, RobustKnock, minimal cut sets, OptCouple) and cameo (heuristic knockout and FSEOF…

GPTomics/bioSkills

Reconstructs B-cell clonal families, quantifies somatic hypermutation and selection, and builds antibody lineage trees with the Immcantation R suite (alakazam, shazam, scoper, dowser, tigger) on…

GPTomics/bioSkills

Align V(D)J reads and assemble TCR/BCR clonotypes with MiXCR, driven by a chemistry-matched preset.

GPTomics/bioSkills

Integrates single-cell paired TCR/BCR (10x VDJ, AIRR, dandelion, BD Rhapsody) with gene expression in an AnnData/MuData object using scirpy - chain-pairing QC, clonotype definition, clonal…

GPTomics/bioSkills

Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS…

GPTomics/bioSkills

Computes immune-repertoire diversity, clonal structure, overlap, and segment usage from TCR/BCR clonotype tables with VDJtools (immunarch as the modern R alternative).

GPTomics/bioSkills

Compares how a rhythm CHANGES between conditions, genotypes, treatments, tissues, or ages (differential rhythmicity), classifying each feature as gain-of-rhythm, loss-of-rhythm, phase change…

GPTomics/bioSkills

Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives…

GPTomics/bioSkills

Estimates tumor fraction (the genome-wide proportion of cfDNA molecules that are tumor-derived, the cfDNA analogue of bulk-tumor purity) from shallow whole-genome sequencing with ichorCNA, an HMM…

GPTomics/bioSkills

Call germline SNPs and indels from a BAM/CRAM with bcftools mpileup and call, and select the right calling engine for the job.

GPTomics/bioSkills

Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification over multi-channel pileup tensors.

GPTomics/bioSkills

Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivity tranches), VETS/ScoreVariantAnnotations, NVScoreVariants, hard filters with…

GPTomics/bioSkills

Combine, split, sort, intersect, and subset VCF/BCF files with bcftools merge, concat, isec, sort, view, and reheader.

GPTomics/bioSkills

Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools…

GPTomics/bioSkills

Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on…

GPTomics/bioSkills

Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed.

GPTomics/bioSkills

Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and…

GPTomics/bioSkills

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry…

GPTomics/bioSkills

Authors bioinformatics pipelines in WDL (Workflow Description Language) run by Cromwell or miniwdl, targeting the GATK/Broad and Terra/AnVIL/BioData Catalyst cloud ecosystem, with tasks, workflows…

GPTomics/bioSkills

Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5…

GPTomics/bioSkills

Orchestrates the end-to-end ChIP-seq pipeline from FASTQ to blacklist-filtered, annotated peaks, chaining fastp QC, Bowtie2 alignment, pre-dedup library-complexity QC (NRF/PBC), duplicate removal…

GPTomics/bioSkills

Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs.

GPTomics/bioSkills

Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it.

GPTomics/bioSkills

Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missingness, controls-only HWE, KING relatedness), panel harmonization + joint…

GPTomics/bioSkills

End-to-end Hi-C analysis workflow from FASTQ to compartments, TADs, and loops, with the decision of WHICH features the sequencing depth can support.

GPTomics/bioSkills

Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification…

GPTomics/bioSkills

Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining pre-analytic QC, UMI/duplex…

GPTomics/bioSkills

Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling…

GPTomics/bioSkills

Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO…

GPTomics/bioSkills

Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality…

GPTomics/bioSkills

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and…

GPTomics/bioSkills

Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation…

GPTomics/bioSkills

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC…

GPTomics/bioSkills

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) +…

GPTomics/bioSkills

Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein abundance with limma/DEqMS/MSstats.

GPTomics/bioSkills

Orchestrates the end-to-end bulk RNA-seq differential-expression pipeline from FASTQ to an annotated DE gene table, chaining fastp QC/trim, Salmon (decoy-aware) or STAR+featureCounts quantification…

GPTomics/bioSkills

Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chaining ambient-RNA removal, doublet detection, MAD-adaptive QC, normalization…

GPTomics/bioSkills

Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets, chaining kit-aware cutadapt trimming (adapter on every read, UMI/4N handling)…

GPTomics/bioSkills

Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and statistics, branching FIRST on platform class (imaging in-situ…

GPTomics/bioSkills

Orchestrates the end-to-end bulk short-read alternative-splicing pipeline from FASTQ to differential splicing, chaining fastp QC, cohort-consistent STAR 2-pass alignment (one shared junction DB)…

GPTomics/bioSkills

Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks.

GPTomics/bioSkills

Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4…

GPTomics/bioSkills