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

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bamip/baminput control +…

GPTomics/bioSkills

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel…

GPTomics/bioSkills

Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal).

GPTomics/bioSkills

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking…

GPTomics/bioSkills

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools…

GPTomics/bioSkills

Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS.

GPTomics/bioSkills

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST.

GPTomics/bioSkills

Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the…

GPTomics/bioSkills

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML.

GPTomics/bioSkills

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

GPTomics/bioSkills

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX…

GPTomics/bioSkills

Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence).

GPTomics/bioSkills

Nominates and assesses CRISPR off-target sites genome-wide. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model.

GPTomics/bioSkills

Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries…

GPTomics/bioSkills

Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic…

GPTomics/bioSkills

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set.

GPTomics/bioSkills

Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismarkmethylationextractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the…

GPTomics/bioSkills

Estimates cell-type composition from bulk DNA methylation and uses it to defuse the single biggest EWAS confounder.

GPTomics/bioSkills

Tests individual CpG sites for differential methylation (DMC/DMP) from bisulfite sequencing counts or array/continuous beta-value matrices.

GPTomics/bioSkills

Detects differentially methylated regions (DMRs) from short-read bisulfite (WGBS/RRBS), array, and long-read methylation count tables using dmrseq (permutation region-FDR over the region selection)…

GPTomics/bioSkills

Designs and defends an epigenome-wide association study (EWAS) on 450K/EPIC array or bisulfite methylation - the layer deciding whether a hit is credible.

GPTomics/bioSkills

Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removing primers with cutadapt (--discard-untrimmed), learning a per-run error model…

GPTomics/bioSkills

Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative), ANCOM-BC2/ANCOMBC…

GPTomics/bioSkills

Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenness, Faith PD, Bray-Curtis, Jaccard, weighted/unweighted/generalized UniFrac…

GPTomics/bioSkills

Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic interpolation of reference-genome gene content - EPA-ng placement, gappa, castor…

GPTomics/bioSkills

Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality]…

GPTomics/bioSkills

Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and primer region - DADA2 assignTaxonomy + addSpecies (RDP naive Bayes), DECIPHER IDTAXA…

GPTomics/bioSkills

Harmonizes already-normalized per-omic matrices onto a common footing before joint integration - assembling a MultiAssayExperiment, choosing the per-omic variance-stabilizing transform, deciding…

GPTomics/bioSkills

Chooses a bulk multi-omics integration strategy before any tool runs by mapping the biological question (subtype discovery, shared axis of variation, predictive signature, pairwise correlation) to a…

GPTomics/bioSkills

Turns an enrichResult or gseaResult from clusterProfiler/enrichplot into a figure that collapses or shows gene-set redundancy, using dotplot, barplot, cnetplot, emapplot, treeplot, ridgeplot…

GPTomics/bioSkills

Tests gene lists, ranked vectors, and fold-change vectors against KEGG pathways and modules with clusterProfiler enrichKEGG/enrichMKEGG (ORA), gseKEGG (GSEA), and SPIA/graphite (signed-topology…

GPTomics/bioSkills

Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes…

GPTomics/bioSkills

Estimate divergence times under molecular-clock models with BEAST2, MCMCTree/PAML, TreePL, and LSD2, framing a date as a product of the calibration prior and the clock model far more than of the…

GPTomics/bioSkills

Infers maximum-likelihood phylogenetic trees with IQ-TREE2 and RAxML-NG -- model selection (ModelFinder), branch support (UFBoot2, SH-aLRT), concordance factors (gCF/sCF), partitioning, topology…

GPTomics/bioSkills

Estimates species trees under the multispecies coalescent from per-locus gene trees with the modern ASTER astral binary (ASTRAL-III/wASTRAL/ASTRAL-Pro), plus SVDQuartets, BPP, and StarBEAST2.

GPTomics/bioSkills

Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based clustering (ADMIXTURE, fastSTRUCTURE), FST estimators (Weir-Cockerham vs Hudson), and…

GPTomics/bioSkills

Scans genomes for natural selection with SFS tests (Tajima's D, Fay & Wu H, Zeng E, SweepFinder2 CLR), haplotype tests (iHS, nSL, XP-EHH, Rsb, H12), and differentiation (FST, PBS) using…

GPTomics/bioSkills

Designs and ranks PCR primer pairs for a target template with primer3-py (designprimers), returning pairs with nearest-neighbor Tm, GC, product size, and complementarity scores.

GPTomics/bioSkills

Analyzes data-independent acquisition (DIA) proteomics by scoring reconstructed fragment-chromatogram peak groups against a decoy null with DIA-NN (library-free directDIA, library-based, or…

GPTomics/bioSkills

Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives.

GPTomics/bioSkills