Agent skills by GPTomics, page 10

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

End-to-end biomarker discovery workflow from expression data to validated biomarker panels.

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 the copy-number pipeline from BAM to segmented, integer-called, annotated CNVs, forking on germline-vs-somatic - CNVkit (somatic exome/panel: coverage - assay-matched reference/PoN -…

GPTomics/bioSkills

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

GPTomics/bioSkills

End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations.

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

Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics…

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

End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation efficiency, and stalling.

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

Analyzes base-editing screens for variant function. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for…

GPTomics/bioSkills

Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing…

GPTomics/bioSkills

Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier…

GPTomics/bioSkills

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework.

GPTomics/bioSkills

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure.

GPTomics/bioSkills

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via…

GPTomics/bioSkills

Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired…

GPTomics/bioSkills

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via…

GPTomics/bioSkills

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer…

GPTomics/bioSkills

Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP…

GPTomics/bioSkills

Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI…

GPTomics/bioSkills

Assigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom…

GPTomics/bioSkills

Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number Re, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2…

GPTomics/bioSkills

Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV…

GPTomics/bioSkills

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice)…

GPTomics/bioSkills