Agent skills by GPTomics, page 7

Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and…

GPTomics/bioSkills

Profiles the functional potential of shotgun metagenomes with HUMAnN 3's tiered search (MetaPhlAn prescreen, Bowtie2 pangenome, translated DIAMOND vs UniRef), giving gene-family (RPK) and MetaCyc…

GPTomics/bioSkills

Classifies shotgun metagenomic reads to taxa with Kraken2's minimizer/LCA matching against a chosen reference database, then hands off to Bracken for abundance re-estimation.

GPTomics/bioSkills

Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads).

GPTomics/bioSkills

Resolves and compares bacterial strains below the species level from shotgun metagenomes with inStrain (popANI/conANI microdiversity), StrainPhlAn (marker-SNV consensus phylogeny and nGD), MIDAS2…

GPTomics/bioSkills

Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and…

GPTomics/bioSkills

Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet - MethylSet - GenomicRatioSet).

GPTomics/bioSkills

Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust.

GPTomics/bioSkills

Detects cancer and infers tissue-of-origin from cfDNA methylation by choosing conversion chemistry (bisulfite vs EM-seq vs TAPS vs cfMeDIP), calling read-level methylation haplotypes rather than…

GPTomics/bioSkills

Aligns bisulfite-converted (WGBS, RRBS, PBAT) and enzymatic (EM-seq) short reads to an in-silico C-T/G-A-converted reference with Bismark (Bowtie2 or HISAT2), preparing the genome index, choosing…

GPTomics/bioSkills

Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methylCIPHER.

GPTomics/bioSkills

Imports Bismark coverage or cytosine-report files into the methylKit object model, then runs the import-to-results spine - filterByCoverage, normalizeCoverage, unite/destrand, calculateDiffMeth…

GPTomics/bioSkills

Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception…

GPTomics/bioSkills

Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization…

GPTomics/bioSkills

Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring.

GPTomics/bioSkills

Builds supervised and unsupervised multivariate integration across bulk omics blocks with mixOmics - sPLS for sparse pairwise correlation, DIABLO (block.splsda) for a multi-block discriminant…

GPTomics/bioSkills

Discovers shared and view-specific latent factors across bulk multi-omics blocks (RNA-seq, proteomics, methylation) on a common sample axis with MOFA2's unsupervised Bayesian group factor model…

GPTomics/bioSkills

Stratifies patients into multi-omics subtypes by building one patient-by-patient similarity network per omic, fusing them with SNF's cross-network diffusion, and spectral-clustering the fused graph…

GPTomics/bioSkills

Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized.

GPTomics/bioSkills

Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE).

GPTomics/bioSkills

Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterProfiler's gseGO, gseKEGG, gsePathway, and GSEA (fgseaMultilevel engine), and…

GPTomics/bioSkills

Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-reviewed, reaction-level pathways using ReactomePA's enrichPathway (ORA) and…

GPTomics/bioSkills

Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways.

GPTomics/bioSkills

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al.

GPTomics/bioSkills

Assesses and filters phasing/imputation output - the quality metrics (Beagle DR2, Minimac R2 and EmpRsq, IMPUTE/GLIMPSE INFO), MAF-stratified filtering, true accuracy by masking, the…

GPTomics/bioSkills

Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio.Phylo plus R ape/phangorn/FastME.

GPTomics/bioSkills

Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (treeio, DendroPy) when metadata matters.

GPTomics/bioSkills

Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rather than a display choice.

GPTomics/bioSkills

Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL.

GPTomics/bioSkills

Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA).

GPTomics/bioSkills

Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary statistics to lead SNPs, and defines haplotype blocks with PLINK 1.9/2.0 and…

GPTomics/bioSkills

Manages PLINK genotype filesets - format conversion (VCF, BED/BIM/FAM, PED/MAP, pgen/pvar/psam) and sample/variant QC (missingness, MAF, HWE, sex check, heterozygosity, KING relatedness) with PLINK…

GPTomics/bioSkills

Gene and region-based rare-variant aggregation - burden/collapsing, SKAT, SKAT-O, ACAT-V/ACAT-O, annotation-weighted STAAR - with regenie (--vc-tests), SAIGE-GENE+, and the SKAT R package.

GPTomics/bioSkills

In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D…

GPTomics/bioSkills

Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and…

GPTomics/bioSkills

Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability…

GPTomics/bioSkills

Validates chosen PCR/qPCR oligos for intramolecular thermodynamic liabilities with primer3-py - hairpins, self-dimers, cross-dimers (calchairpin/homodimer/heterodimer), and 3'-end stability…

GPTomics/bioSkills

Co-designs qPCR/RT-qPCR primers and hydrolysis (TaqMan) or molecular-beacon probes with primer3-py (PRIMERPICKINTERNALOLIGO, PRIMERINTERNAL tags), for assays whose deliverable is a quantitative…

GPTomics/bioSkills

Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex…

GPTomics/bioSkills

Loads mass-spectrometry data into Python/R and strips the search engine's bookkeeping before any number is trusted -- removes decoys (REV/Reverse), contaminants (CON/Potential contaminant)…

GPTomics/bioSkills

Groups proteins from peptide identifications and controls protein-level FDR, framing inference as a chosen explanation (parsimony or a probability model) of underdetermined peptide evidence rather…

GPTomics/bioSkills

Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA…

GPTomics/bioSkills

Aligns DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align) vs local (soft-clip read ends) mode and a sensitivity preset; the de-facto aligner for ChIP-seq…

GPTomics/bioSkills

Aligns DNA short reads (paired- or single-end) to a reference genome with bwa-mem2, the maintained successor to BWA-MEM, for WGS/WES and germline/somatic variant-calling pipelines; covers index…

GPTomics/bioSkills

Aligns RNA-seq reads to a genome with HISAT2, the splice-aware aligner whose hierarchical graph FM-index runs at roughly a quarter of STAR's memory (~7 GB for human), whose SNP/haplotype graph index…

GPTomics/bioSkills

Aligns RNA-seq reads to a genome with STAR, the fast splice-aware aligner whose splice-junction database (built from a GTF at sjdbOverhang = readlength-1) and two-pass mode set junction sensitivity…

GPTomics/bioSkills

Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-RNA 3' adapters, amplicon primers, and anchored/linked adapters.

GPTomics/bioSkills

Detects contamination in sequencing reads - cross-species (FastQ Screen, Kraken2), vector/PhiX/adapter, rRNA, and same-species cross-sample/index-hopping and sample swaps (SNP fingerprints via…

GPTomics/bioSkills