Browse Skills — Page 44

bio-gene-regulatory-networks-differential-networks

GPTomics/bioSkills

Compare gene regulatory and co-expression networks between biological conditions to identify rewired regulatory relationships using DiffCorr. Detects gained, lost, and reversed gene-gene correlations between conditions. Use when comparing co-expression networks between disease vs control, treatment conditions, or developmental stages.

bio-gene-regulatory-networks-multiomics-grn

GPTomics/bioSkills

Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking transcription factors to enhancers and target genes. Use when analyzing 10x multiome or paired scRNA+scATAC data to infer cis-regulatory GRNs.

bio-gene-regulatory-networks-perturbation-simulation

GPTomics/bioSkills

Simulate transcription factor perturbation effects on cell state using CellOracle, which integrates GRN inference with in silico knockout and overexpression modeling. Predicts cell identity shifts and differentiation trajectory changes from TF perturbations. Use when predicting the effect of transcription factor knockouts, planning perturbation experiments, or identifying driver TFs for cell fate transitions.

bio-gene-regulatory-networks-scenic-regulons

GPTomics/bioSkills

Infer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression modules with GRNBoost2, prunes by cis-regulatory motif enrichment, and scores regulon activity per cell with AUCell. Use when identifying transcription factor regulons, scoring TF activity in single cells, or finding master regulators of cell identity.

bio-genome-annotation-annotation-transfer

GPTomics/bioSkills

Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.

bio-genome-annotation-eukaryotic-gene-prediction

GPTomics/bioSkills

Predict protein-coding genes in eukaryotic genomes using BRAKER3 for combined RNA-seq and protein evidence, or GALBA for protein-only evidence. Runs Augustus with trained parameters for accurate gene models. Use when annotating a newly assembled eukaryotic genome or improving existing gene predictions.

bio-genome-annotation-functional-annotation

GPTomics/bioSkills

Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted proteins using eggNOG-mapper and InterProScan. Produces functional summaries for downstream pathway and enrichment analysis. Use when adding functional annotation to predicted genes or characterizing protein functions in a new genome.

bio-genome-annotation-ncrna-annotation

GPTomics/bioSkills

Identify non-coding RNAs including tRNAs, rRNAs, snoRNAs, and regulatory RNAs using Infernal covariance model searches against Rfam and tRNAscan-SE for tRNA prediction. Use when performing genome-wide ncRNA annotation with assembly input producing GFF output.

bio-genome-annotation-prokaryotic-annotation

GPTomics/bioSkills

Annotate bacterial and archaeal genomes with Bakta for comprehensive structural and functional annotation, or Prokka for lightweight annotation. Generates GFF3, GenBank, and FASTA outputs with NCBI-compatible locus tags. Use when annotating a newly assembled prokaryotic genome or preparing annotations for NCBI submission.

bio-genome-annotation-repeat-annotation

GPTomics/bioSkills

Identify and classify repetitive elements and transposable elements using RepeatModeler for de novo repeat library construction and RepeatMasker for genome-wide repeat annotation. Quantify TE expression from RNA-seq with TEtranscripts. Use when masking repeats before gene prediction or analyzing transposable element activity.

bio-genome-assembly-assembly-polishing

GPTomics/bioSkills

Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.

bio-genome-assembly-assembly-qc

GPTomics/bioSkills

Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.

bio-genome-assembly-contamination-detection

GPTomics/bioSkills

Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.

bio-genome-assembly-hifi-assembly

GPTomics/bioSkills

High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.

bio-genome-assembly-long-read-assembly

GPTomics/bioSkills

De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.

bio-genome-assembly-metagenome-assembly

GPTomics/bioSkills

Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.

bio-genome-assembly-scaffolding

GPTomics/bioSkills

Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies.

bio-genome-assembly-short-read-assembly

GPTomics/bioSkills

De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.

bio-genome-engineering-base-editing-design

GPTomics/bioSkills

Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.

bio-genome-engineering-grna-design

GPTomics/bioSkills

Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models. Use when designing sgRNAs for gene knockout, activation, or repression experiments.

bio-genome-engineering-hdr-template-design

GPTomics/bioSkills

Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.

bio-genome-engineering-off-target-prediction

GPTomics/bioSkills

Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk.

bio-genome-engineering-prime-editing-design

GPTomics/bioSkills

Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations.

bio-genome-intervals-bed-file-basics

GPTomics/bioSkills

BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.

bio-genome-intervals-bigwig-tracks

GPTomics/bioSkills

Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.

bio-genome-intervals-coverage-analysis

GPTomics/bioSkills

Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.

bio-genome-intervals-gtf-gff-handling

GPTomics/bioSkills

Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.

bio-genome-intervals-interval-arithmetic

GPTomics/bioSkills

Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files.

bio-genome-intervals-proximity-operations

GPTomics/bioSkills

Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features.

bio-geo-data

GPTomics/bioSkills

Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.

bio-hi-c-analysis-compartment-analysis

GPTomics/bioSkills

Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.

bio-hi-c-analysis-contact-pairs

GPTomics/bioSkills

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.

bio-hi-c-analysis-hic-data-io

GPTomics/bioSkills

Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.

bio-hi-c-analysis-hic-differential

GPTomics/bioSkills

Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.

bio-hi-c-analysis-hic-visualization

GPTomics/bioSkills

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.

bio-hi-c-analysis-loop-calling

GPTomics/bioSkills

Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.

bio-hi-c-analysis-matrix-operations

GPTomics/bioSkills

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

bio-hi-c-analysis-tad-detection

GPTomics/bioSkills

Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.

bio-imaging-mass-cytometry-cell-segmentation

GPTomics/bioSkills

Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.

bio-imaging-mass-cytometry-data-preprocessing

GPTomics/bioSkills

Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.

bio-imaging-mass-cytometry-interactive-annotation

GPTomics/bioSkills

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

bio-imaging-mass-cytometry-phenotyping

GPTomics/bioSkills

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

bio-imaging-mass-cytometry-quality-metrics

GPTomics/bioSkills

Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.

bio-imaging-mass-cytometry-spatial-analysis

GPTomics/bioSkills

Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for neighborhood enrichment, or identifying cell-cell interaction patterns in imaging mass cytometry data.

bio-immunoinformatics-epitope-prediction

GPTomics/bioSkills

Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.

bio-immunoinformatics-immunogenicity-scoring

GPTomics/bioSkills

Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.

bio-immunoinformatics-mhc-binding-prediction

GPTomics/bioSkills

Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.

bio-immunoinformatics-neoantigen-prediction

GPTomics/bioSkills

Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses. Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.

bio-immunoinformatics-tcr-epitope-binding

GPTomics/bioSkills

Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitopes or predict TCR targets. Use when analyzing TCR repertoire specificity or identifying antigen-reactive T-cells.

bio-interaction-databases

GPTomics/bioSkills

Query protein-protein and gene interaction databases including STRING, BioGRID, and IntAct via their REST APIs and Python clients. Retrieve interaction networks, confidence scores, and functional enrichment. Use when building protein interaction networks, contextualizing gene lists with known interactions, or retrieving pathway-level interaction data.

bio-isoform-switching

GPTomics/bioSkills

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

bio-liquid-biopsy-pipeline

GPTomics/bioSkills

Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.

bio-local-blast

GPTomics/bioSkills

Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NCBI servers are slow or unavailable.

bio-long-read-sequencing-clair3-variants

GPTomics/bioSkills

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

bio-long-read-sequencing-isoseq-analysis

GPTomics/bioSkills

Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.

bio-long-read-sequencing-nanopore-methylation

GPTomics/bioSkills

Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.

bio-long-read-splicing

GPTomics/bioSkills

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

bio-longitudinal-monitoring

GPTomics/bioSkills

Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or detecting molecular relapse before clinical progression.

bio-longread-alignment

GPTomics/bioSkills

Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.

bio-longread-medaka

GPTomics/bioSkills

Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.

bio-longread-qc

GPTomics/bioSkills

Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.

bio-longread-structural-variants

GPTomics/bioSkills

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.

bio-machine-learning-atlas-mapping

GPTomics/bioSkills

Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without retraining on combined data. Use when annotating new single-cell datasets using pre-trained reference models.

bio-machine-learning-biomarker-discovery

GPTomics/bioSkills

Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data.

bio-machine-learning-model-validation

GPTomics/bioSkills

Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfitting in biomarker discovery. Use when validating classifiers or optimizing hyperparameters on omics data.

bio-machine-learning-omics-classifiers

GPTomics/bioSkills

Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs. Includes proper preprocessing and evaluation metrics for biomarker classifiers. Use when building diagnostic or prognostic classifiers from expression or variant data.

bio-machine-learning-prediction-explanation

GPTomics/bioSkills

Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions. Use when interpreting biomarker classifiers or understanding model predictions.

bio-machine-learning-survival-analysis

GPTomics/bioSkills

Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.

bio-metabolomics-lipidomics

GPTomics/bioSkills

Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.

bio-metabolomics-metabolite-annotation

GPTomics/bioSkills

Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.

bio-metabolomics-msdial-preprocessing

GPTomics/bioSkills

MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.

bio-metabolomics-normalization-qc

GPTomics/bioSkills

Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.

bio-metabolomics-pathway-mapping

GPTomics/bioSkills

Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.

bio-metabolomics-statistical-analysis

GPTomics/bioSkills

Statistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes, Welch's t-tests with BH correction, fold change estimation, and multivariate methods (PCA, PLS-DA, OPLS-DA). Use when identifying differentially abundant metabolites or building classification models.

bio-metabolomics-targeted-analysis

GPTomics/bioSkills

Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves and internal standards.

bio-metabolomics-xcms-preprocessing

GPTomics/bioSkills

XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.

bio-metagenomics-abundance

GPTomics/bioSkills

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.

bio-metagenomics-amr-detection

GPTomics/bioSkills

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

bio-metagenomics-functional-profiling

GPTomics/bioSkills

Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.

bio-metagenomics-kraken

GPTomics/bioSkills

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.

bio-metagenomics-metaphlan

GPTomics/bioSkills

Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.

bio-metagenomics-strain-tracking

GPTomics/bioSkills

Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.

bio-metagenomics-visualization

GPTomics/bioSkills

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.

bio-methylation-based-detection

GPTomics/bioSkills

Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease.

bio-methylation-bismark-alignment

GPTomics/bioSkills

Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.

bio-methylation-calling

GPTomics/bioSkills

Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.

bio-methylation-differential-cpg

GPTomics/bioSkills

Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage filtering, statistical tests (Welch t-test, Mann-Whitney, limma, DSS beta-binomial), multiple testing correction, and effect size calculation. Use when comparing methylation at individual CpG sites between experimental groups from WGBS, RRBS, or targeted bisulfite sequencing.

bio-methylation-dmr-detection

GPTomics/bioSkills

Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.

bio-methylation-methylkit

GPTomics/bioSkills

DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.

bio-microbiome-amplicon-processing

GPTomics/bioSkills

Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.

bio-microbiome-differential-abundance

GPTomics/bioSkills

Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.

bio-microbiome-diversity-analysis

GPTomics/bioSkills

Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.

bio-microbiome-functional-prediction

GPTomics/bioSkills

Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.

bio-microbiome-qiime2-workflow

GPTomics/bioSkills

QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.

bio-microbiome-taxonomy-assignment

GPTomics/bioSkills

Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.

bio-molecular-descriptors

GPTomics/bioSkills

Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.

bio-molecular-io

GPTomics/bioSkills

Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.

bio-motif-search

GPTomics/bioSkills

Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme analysis, use the restriction-analysis skill.

bio-multi-omics-data-harmonization

GPTomics/bioSkills

Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.

bio-multi-omics-mixomics-analysis

GPTomics/bioSkills

Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate between groups.