Research & Science · 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 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

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

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

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

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

Runs all-in-one FASTQ preprocessing with fastp in a single pass - adapter trimming via paired-end overlap analysis, quality/length filtering, 2-color poly-G removal, base correction, optional…

GPTomics/bioSkills

Filters reads by quality, length, N content, and complexity with Trimmomatic, fastp, and Cutadapt, including sliding-window trimming, per-read unqualified-base filtering, and 2-color poly-G removal.

GPTomics/bioSkills

Generates and interprets per-file and cross-sample QC reports from FASTQ data with FastQC, falco, and MultiQC, covering Phred quality, per-base composition, GC, duplication, overrepresented…

GPTomics/bioSkills

Runs RNA-seq-specific post-alignment QC - strandedness inference, gene-body 5'-3' coverage, read distribution (exonic/intronic/intergenic), rRNA/globin/mitochondrial rate, transcript integrity…

GPTomics/bioSkills

Extracts UMIs and collapses reads to original molecules with umitools (directional dedup) or builds error-corrected single-strand/duplex consensus reads with fgbio.

GPTomics/bioSkills

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access.

GPTomics/bioSkills

Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one interactive MultiQC report, and guides module scoping, sample-name resolution…

GPTomics/bioSkills

Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2.

GPTomics/bioSkills

Select restriction enzymes for cloning or diagnostics using Biopython Bio.Restriction.

GPTomics/bioSkills

Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction.

GPTomics/bioSkills

Design and validate Type IIS scarless DNA assembly (Golden Gate, MoClo) using Biopython Bio.Restriction.

GPTomics/bioSkills

Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction.

GPTomics/bioSkills

Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction.

GPTomics/bioSkills

Performs retrosynthetic planning using AiZynthFinder (template-based MCTS), maintained or version-pinned template-free models, ASKCOS, and emerging RetroSynFormer with explicit handling of route…

GPTomics/bioSkills

Generate reverse complements and complements of DNA/RNA sequences using Biopython, including IUPAC ambiguity codes, gapped alignments, and minus-strand features.

GPTomics/bioSkills

Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing genome mapping.

GPTomics/bioSkills

Quality control and exploration of RNA-seq count matrices before differential expression.

GPTomics/bioSkills

Tests whether a proposed or predicted RNA secondary structure is supported by evolutionary covariation using R-scape, which scores compensatory substitutions against a phylogeny-aware null and…

GPTomics/bioSkills

Searches for non-coding RNA homologs and classifies RNA families with Infernal covariance models against Rfam, scoring sequence AND secondary-structure conservation jointly.

GPTomics/bioSkills

Processes experimental RNA structure probing data (SHAPE-MaP, DMS-MaPseq) into per-nucleotide reactivity profiles with ShapeMapper2, then uses them as soft restraints on thermodynamic folding.

GPTomics/bioSkills

Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython.

GPTomics/bioSkills