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SkillsMP has collected 562 skills from GPTomics/bioSkills. Open a skill to review its source and details.
GPTomics/bioSkillsShowing 40 of 562 collected skills.
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 tests, and long-branch-attraction control. Covers why an ML tree…
Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rather than a display choice. Covers why most inference returns an unrooted tree so placing the root creates every ancestor/descendant and basal…
Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL. Covers why a tree figure is an argument not a neutral picture, the cladogram-vs-phylogram-vs-chronogram choice that hides or reveals rate and…
Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA). A GWAS statistic is valid only when genotype is independent of unmodeled phenotype drivers after the chosen…
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, chromatogram, and in-silico predicted libraries via Koina-served…
Assign cells to their sample of origin from cell or nucleus hashing (CITE-seq HTOs, MULTI-seq lipid/cholesterol tags, CellPlex CMOs) and call cross-sample doublets using Seurat HTODemux/MULTIseqDemux, hashsolo, demuxEM, GMM-Demux, and demuxmix. Use when…
Loads spatial transcriptomics data from Visium, Visium HD, Xenium, MERFISH/MERSCOPE, CosMx, Slide-seq/Curio, and Stereo-seq into AnnData or SpatialData using spatialdata-io and Squidpy. Use when deciding which platform class is in hand (imaging/in-situ vs…
Identify spatially coherent tissue domains (regions like cortical layers, tumor vs stroma) in Visium, Visium HD, Xenium, MERFISH, Slide-seq, and Stereo-seq data with Squidpy, BANKSY, BayesSpace, STAGATE, and GraphST. Use when distinguishing a domain (a region…
Build the spatial neighbor graph that every downstream spatial statistic (Moran's I, neighborhood enrichment, co-occurrence, spatial domains) inherits, using Squidpy. Use when choosing the graph type (kNN vs Delaunay vs fixed-radius vs Visium hex grid) and…
Reconstructs B-cell clonal families, quantifies somatic hypermutation and selection, and builds antibody lineage trees with the Immcantation R suite (alakazam, shazam, scoper, dowser, tigger) on AIRR-format BCR data. Use when deriving the clonal-clustering…
Tests and estimates rhythmicity at a PRE-SPECIFIED period (canonically 24h) in time-series omics using cosinor regression (CosinorPy), JTK_CYCLE/ARSER/Lomb-Scargle meta-analysis (MetaCycle meta2d), and non-parametric tests for asymmetric waveforms (RAIN,…
Compares how a rhythm CHANGES between conditions, genotypes, treatments, tissues, or ages (differential rhythmicity), classifying each feature as gain-of-rhythm, loss-of-rhythm, phase change, amplitude change, unchanged-rhythmic, or arrhythmic-in-both, and…
Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele,…
Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR. Use when deciding which annotation engine and version to pin, which transcript set to report…
Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL…
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, leakage-safe cross-validation, calibration, and SHAP interpretation. Use when building and validating diagnostic or…
Orchestrates the copy-number pipeline from BAM to segmented, integer-called, annotated CNVs, forking on germline-vs-somatic - CNVkit (somatic exome/panel: coverage -> assay-matched reference/PoN -> fix -> segment -> purity/ploidy-aware call), GATK gCNV…
Orchestrates an end-to-end CRISPR editing experiment design from target gene to delivery-ready, validatable constructs. Sequences guide design, off-target assessment, edit-modality selection (knockout, base editing, prime editing, HDR knock-in), and…
End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations. Orchestrates the read -> compensate/unmix -> transform -> QC -> doublet-removal -> cluster-or-gate -> annotate -> diffcyt…
End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as…
Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA,…
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 (bcftools/GATK HaplotypeCaller/DeepVariant/DRAGEN),…
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 -> ncRNA), then eggNOG/InterProScan functional assignment…
Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it. Profiles the genome first (k-mer spectrum -> size, heterozygosity, ploidy), QCs reads, chooses an assembly path by data…
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 cisTopic -> pycistarget -> eGRN), and CellOracle perturbation.…
Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missingness, controls-only HWE, KING relatedness), panel harmonization + joint phasing/imputation to dosages, long-range-LD-excluded PCA, and an…
End-to-end Hi-C analysis workflow from FASTQ to compartments, TADs, and loops, with the decision of WHICH features the sequencing depth can support. Covers pairtools read-pair processing and library QC, cooler matrices, ICE balancing and distance-decay…
Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification, phenotyping, and squidpy spatial statistics. Use when committing the…
Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining pre-analytic QC, UMI/duplex error-suppression (fgbio), fragment QC, ichorCNA tumor…
Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari…
Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance +…
Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality, and context-specific models. Use when committing the…
Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics, background-aware pathway mapping), naming what each stage decides and…
End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering,…
Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation calling, methylKit coverage-filtering/normalization, and…
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 (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy…
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 (predictive signature), or SNF (patient subtypes). Use when…
Orchestrates genomic-epidemiology outbreak investigation from pathogen isolates to transmission networks, forking bacterial (snippy -> Gubbins recombination-masking -> IQ-TREE -> TreeTime -> TransPhylo) vs viral (Nextstrain/augur), with parallel MLST typing…
Orchestrates bottom-up proteomics from a search engine's output (MaxQuant/FragPipe/DIA-NN) to differential protein abundance with limma/DEqMS/MSstats. Use when committing the search database + acquisition mode (DDA vs DIA) up front, re-controlling FDR at PSM…
End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation efficiency, and stalling. Use when orchestrating a full ribosome profiling pipeline and deciding harvest/dedup/alignment options and which…