By GPTomics

Peptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than a raw engine score (XCorr, hyperscore…

GPTomics/bioSkills

Quality control for bottom-up proteomics across three levels -- instrument/raw-signal (mass accuracy, RT/iRT fit, FWHM, TIC vs injection time, % MS2 identified), identification/run (missed…

GPTomics/bioSkills

Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with…

GPTomics/bioSkills

Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/iTRAQ reporter ions, MS2 vs SPS-MS3), and metabolic (SILAC) approaches, including…

GPTomics/bioSkills

Predicts RNA secondary structure with ViennaRNA, treating the Boltzmann ensemble (partition function, base-pair probabilities, centroid, MEA, stochastic samples) as the object rather than a single…

GPTomics/bioSkills

Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence with Bio.PDB.

GPTomics/bioSkills

Tests and estimates rhythmicity at a PRE-SPECIFIED period (canonically 24h) in time-series omics using cosinor regression (CosinorPy), JTKCYCLE/ARSER/Lomb-Scargle meta-analysis (MetaCycle meta2d)…

GPTomics/bioSkills

Discovers a periodic signal of UNKNOWN period in time-series omics data and puts a defensible significance on it, especially when sampling is IRREGULAR (dropped timepoints, pooled harvests) so…

GPTomics/bioSkills

Clusters temporally variable genes by expression-profile SHAPE (not significance) using Mfuzz fuzzy c-means, TCseq, DEGreport degPatterns, and tslearn DTW/soft-DTW.

GPTomics/bioSkills

Models continuous temporal trajectories from BULK or time-resolved omics where the x-axis is measured experimental time: penalized GAMs (mgcv) for smooth trends and changepoint detection (segmented…

GPTomics/bioSkills

Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR.

GPTomics/bioSkills

Classify variant clinical significance with the ACMG/AMP germline framework and its 2018-2025 ClinGen refinements (graded PVS1 decision tree, PM2 downgraded to Supporting, PP5/BP6 retired…

GPTomics/bioSkills

Joint genotype a cohort of per-sample gVCFs with GATK (HaplotypeCaller -ERC GVCF - GenomicsDBImport or CombineGVCFs - GenotypeGVCFs) or GLnexus for DeepVariant gVCFs, producing a squared-off…

GPTomics/bioSkills

Call structural variants (=50 bp deletions, insertions, inversions, duplications, translocations) from short- or long-read data by reconstructing four orthogonal signals (discordant pairs, split…

GPTomics/bioSkills

Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants with bcftools norm.

GPTomics/bioSkills

View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2.

GPTomics/bioSkills

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes.

GPTomics/bioSkills

End-to-end eDNA metabarcoding from raw amplicons to community ecology.

GPTomics/bioSkills

Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run…

GPTomics/bioSkills

Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling…

GPTomics/bioSkills

Orchestrates genome annotation from assembled contigs to functional annotation, forking prokaryotic (Bakta one-step, genetic-code table from GTDB-Tk) vs eukaryotic (RepeatMask - BRAKER3 - functional…

GPTomics/bioSkills

Orchestrates gene regulatory network inference from processed single-cell data to regulons and in-silico perturbation, via pySCENIC (RNA-only GRNBoost2 - cisTarget - AUCell), SCENIC+ (multiome…

GPTomics/bioSkills

End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference…

GPTomics/bioSkills

Orchestrates VERTICAL bulk multi-omics integration (RNA + protein + methylation on the SAME samples) from harmonization to a validated result, routing to MOFA2 (shared factors), mixOmics/DIABLO…

GPTomics/bioSkills

Orchestrates genomic-epidemiology outbreak investigation from pathogen isolates to transmission networks, forking bacterial (snippy - Gubbins recombination-masking - IQ-TREE - TreeTime - TransPhylo)…

GPTomics/bioSkills

Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2), wiring the somatic-specific machinery - panel-of-normals and gnomAD…

GPTomics/bioSkills

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment.

GPTomics/bioSkills

Imputes untyped genotypes against a phased reference panel with Beagle, Minimac4, or IMPUTE5 (array data) or from genotype likelihoods with GLIMPSE2, QUILT2, or STITCH (low-coverage WGS), producing…

GPTomics/bioSkills

Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input…

GPTomics/bioSkills

Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, HGDP+1kGP/gnomAD, CAAPA), matching panel ancestry to the target, reconciling…

GPTomics/bioSkills

Builds publication-ready tables - descriptive Table 1, regression and differential-expression result tables, and supplementary tables - with gtsummary, gt, flextable, and kableExtra (R) or…

GPTomics/bioSkills