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SkillsMP hat 604 Skills aus PKU-YuanGroup/OpenAI4S gesammelt. Öffne einen Skill, um Quelle und Details zu prüfen.
PKU-YuanGroup/OpenAI4SEs werden 40 von 604 gesammelten Skills angezeigt.
Predicts protein and complex structures with deep-learning models (ESMFold, AlphaFold2/ColabFold, AlphaFold3, Chai-1, Boltz-1/2) and reconciles them with confidence metrics. Use when choosing a predictor by input and question rather than novelty (ESMFold…
Quellsprache: Englisch
Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that may exceed PDB's ~62-chain / 99,999-atom limits; when residue numbers do not match…
Quellsprache: Englisch
Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities. Use when applying a rotation matrix and needing to know whether it is…
Quellsprache: Englisch
Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hides by default. Use when deciding how to handle altloc/DisorderedAtom conformers before a distance or RMSD, indexing residues…
Quellsprache: Englisch
Prepares a deposited or predicted structure for docking, molecular dynamics, or electrostatics by adding hydrogens, assigning protonation and tautomer states, and filling missing atoms and short loops with PDBFixer, reduce, PROPKA, and PDB2PQR. Use when…
Quellsprache: Englisch
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. Use when deciding if a structure or a specific region is…
Quellsprache: Englisch
Builds and simulates multi-species metabolic community models from member genome-scale models, using MICOM for abundance-weighted steady-state community FBA and cooperative tradeoff, SMETANA for cross-feeding and competition scoring, and SteadyCom/COMETS for…
Quellsprache: Englisch
Builds tissue-, cell-type-, and condition-specific metabolic models by integrating transcriptomic or proteomic data into a generic genome-scale model, using extraction algorithms (GIMME, iMAT, INIT/tINIT, MADE, E-Flux, CORDA, FASTCORE) via troppo and corda in…
Quellsprache: Englisch
Performs flux balance analysis (FBA), flux variability analysis (FVA), parsimonious FBA (pFBA), loopless FBA, flux sampling, and production envelopes on genome-scale metabolic models with COBRApy, solving the biomass-maximization linear program under a…
Quellsprache: Englisch
Performs in-silico single and double gene deletions, condition-dependent essentiality, and synthetic-lethality screens on genome-scale metabolic models with COBRApy, evaluating gene-protein-reaction rules and comparing FBA re-optimization against MOMA/ROOM…
Quellsprache: Englisch
Builds draft genome-scale metabolic models from an annotated genome using CarveMe (top-down carving of a BiGG universal model) or gapseq (bottom-up pathway-evidence reconstruction), then loads and sanity-checks the draft in COBRApy. Use when creating a model…
Quellsprache: Englisch
Validates, gap-fills, and standardizes genome-scale metabolic models using memote for consistency and annotation scoring and COBRApy for manual curation, including mass/charge balance, energy-generating-cycle detection, dead-end resolution, GPR fixes, and…
Quellsprache: Englisch
Computes metabolic-engineering strain designs on genome-scale models with StrainDesign (OptKnock, RobustKnock, minimal cut sets, OptCouple) and cameo (heuristic knockout and FSEOF over/under-expression targets), finding gene/reaction interventions that couple…
Quellsprache: Englisch
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…
Quellsprache: Englisch
Align V(D)J reads and assemble TCR/BCR clonotypes with MiXCR, driven by a chemistry-matched preset. Use when choosing/auditing the preset for a library (5'RACE/template-switch vs multiplex-primer amplicon -> rigid vs floating boundaries; RNA vs gDNA ->…
Quellsprache: Englisch
Draws TCR/BCR repertoire figures - V-J chord/circos, CDR3 spectratype, clonal-space stratification, clonal tracking across timepoints, rarefaction/extrapolation curves, overlap heatmaps, and clonotype-similarity networks - and encodes how to read them. Use…
Quellsprache: Englisch
Integrates single-cell paired TCR/BCR (10x VDJ, AIRR, dandelion, BD Rhapsody) with gene expression in an AnnData/MuData object using scirpy - chain-pairing QC, clonotype definition, clonal expansion, diversity, repertoire overlap, V(D)J usage, and VDJdb…
Quellsprache: Englisch
Maps TCR/BCR receptor sequences toward candidate antigen specificity and clusters repertoires by shared-specificity signal, while enforcing that a database match or a cluster label is a HYPOTHESIS, not a specificity call. Use when deciding among database…
Quellsprache: Englisch
Computes immune-repertoire diversity, clonal structure, overlap, and segment usage from TCR/BCR clonotype tables with VDJtools (immunarch as the modern R alternative). Use when deciding which diversity estimator answers a question (q=0 observed…
Quellsprache: Englisch
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,…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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 FFT/Welch/JTK are invalid. Estimates the dominant period with…
Quellsprache: Englisch
Clusters temporally variable genes by expression-profile SHAPE (not significance) using Mfuzz fuzzy c-means, TCseq, DEGreport degPatterns, and tslearn DTW/soft-DTW. Use when grouping pre-selected time-course genes into shared trajectory programs…
Quellsprache: Englisch
Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives; Random Forests by default, Extra-Trees optional), and dynamic…
Quellsprache: Englisch
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, ruptures) for abrupt regime shifts. Use when deciding…
Quellsprache: Englisch
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, calibrated PP3/BP4, Bayesian points), the AMP/ASCO/CAP somatic tiers…
Quellsprache: Englisch
Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT…
Quellsprache: Englisch
Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification over multi-channel pileup tensors. Covers platform-specific model selection (WGS, WES, PACBIO, ONT_R104, HYBRID_PACBIO_ILLUMINA), one-shot…
Quellsprache: Englisch
Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivity tranches), VETS/ScoreVariantAnnotations, NVScoreVariants, hard filters with per-annotation thresholds, and bcftools/cyvcf2 expressions, plus…
Quellsprache: Englisch
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,…
Quellsprache: Englisch
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 sample-by-site genotype matrix. Use when deciding between joint…
Quellsprache: Englisch
Call structural variants (>=50 bp deletions, insertions, inversions, duplications, translocations) from short- or long-read data by reconstructing four orthogonal signals (discordant pairs, split reads via the SA tag, read depth, local assembly). Covers…
Quellsprache: Englisch
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…
Quellsprache: Englisch
Call germline SNPs and indels from a BAM/CRAM with bcftools mpileup and call, and select the right calling engine for the job. Use when generating a VCF from aligned reads, choosing between bcftools, GATK HaplotypeCaller, DeepVariant, and DRAGEN, setting…
Quellsprache: Englisch
Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants with bcftools norm. Use when comparing variants across callers or cohorts, preparing a VCF for database annotation or ClinVar/dbSNP matching,…
Quellsprache: Englisch
View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2. Use when inspecting variants, extracting fields with query format strings, converting VCF/BCF, or correctly reading a field -- QUAL (site) vs GQ (genotype) vs PL/GL likelihoods, AD vs…
Quellsprache: Englisch
Combine, split, sort, intersect, and subset VCF/BCF files with bcftools merge, concat, isec, sort, view, and reheader. Use when merging different samples into a cohort VCF, concatenating per-chromosome or per-region call sets for the same samples,…
Quellsprache: Englisch
Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools (somalier, peddy, KING). Use when judging whether a callset is…
Quellsprache: Englisch
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…
Quellsprache: Englisch
Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue…
Quellsprache: Englisch