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SkillsMP 已收集 PKU-YuanGroup/OpenAI4S 中的 604 个 Skill。打开任一 Skill 可查看来源和详情。
PKU-YuanGroup/OpenAI4S已展示 40 / 604 个已收集 Skill。
Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, HGDP+1kGP/gnomAD, CAAPA), matching panel ancestry to the target, reconciling genome build and chromosome naming, and running the strand/allele…
原文语言：英语
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, and PhyloBayes-MPI. Covers why convergence (ESS, PSRF, ASDSF,…
原文语言：英语
Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio.Phylo plus R ape/phangorn/FastME. Covers why a distance is a model-corrected estimate of substitutions per site that undercounts raw because…
原文语言：英语
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 sequence data. Covers why branch length = rate x time is…
原文语言：英语
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…
原文语言：英语
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. Covers why a species tree is not a gene tree, why each locus has…
原文语言：英语
Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (treeio, DendroPy) when metadata matters. Covers why a tree file is a lossy serialization, why format conversion silently drops BEAST/MrBayes…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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 scikit-allel. r2 and D' answer different questions - r2 (= chi2/N)…
原文语言：英语
Manages PLINK genotype filesets - format conversion (VCF, BED/BIM/FAM, PED/MAP, pgen/pvar/psam) and sample/variant QC (missingness, MAF, HWE, sex check, heterozygosity, KING relatedness) with PLINK 1.9 and 2.0. PLINK rewrites allele bookkeeping: PLINK 1.x A1…
原文语言：英语
Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based clustering (ADMIXTURE, fastSTRUCTURE), FST estimators (Weir-Cockerham vs Hudson), and f-statistics (f3/f4/D via AdmixTools/admixr), plus Python…
原文语言：英语
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. Single-variant tests are powerless at low minor allele count, so rare…
原文语言：英语
In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D admixture stats, LD pruning, PCA, and selection scans (iHS, XP-EHH,…
原文语言：英语
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 scikit-allel, selscan, and SweepFinder2. No single statistic separates…
原文语言：英语
Designs and ranks PCR primer pairs for a target template with primer3-py (design_primers), returning pairs with nearest-neighbor Tm, GC, product size, and complementarity scores. Covers why primer3 is a LOCAL weighted-penalty minimizer over the single…
原文语言：英语
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 prefilter, against the correct database. Covers why plain BLAST…
原文语言：英语
Validates chosen PCR/qPCR oligos for intramolecular thermodynamic liabilities with primer3-py - hairpins, self-dimers, cross-dimers (calc_hairpin/homodimer/heterodimer), and 3'-end stability (calc_end_stability) - returning ThermoResult dG/Tm and ASCII…
原文语言：英语
Co-designs qPCR/RT-qPCR primers and hydrolysis (TaqMan) or molecular-beacon probes with primer3-py (PRIMER_PICK_INTERNAL_OLIGO, PRIMER_INTERNAL_* tags), for assays whose deliverable is a quantitative measurement device. Covers why amplification efficiency…
原文语言：英语
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), Only-identified-by-site groups, and resolves semicolon…
原文语言：英语
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 deep-learning predicted-library routes), Spectronaut, OpenSWATH, and…
原文语言：英语
Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives. Frames missing values as left-censored MNAR (model, do not impute), makes…
原文语言：英语
Peptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than a raw engine score (XCorr, hyperscore, Andromeda, SpecEValue). Covers sequence-database search…
原文语言：英语
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 than a measurement. Reports protein GROUPS (proteins…
原文语言：英语
Quality control for bottom-up proteomics across three levels -- instrument/raw-signal (mass accuracy, RT/iRT fit, FWHM, TIC vs injection time, % MS2 identified), identification/run (missed cleavages, charge states, PTM handling artifacts, contaminants), and…
原文语言：英语
Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with MSstatsPTM - plus kinase-activity and functional triage. Covers…
原文语言：英语
Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/iTRAQ reporter ions, MS2 vs SPS-MS3), and metabolic (SILAC) approaches, including peptide-to-protein summarization (Tukey median polish,…
原文语言：英语
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…
原文语言：英语
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, ATAC-seq, and CUT&RUN, where fragment-geometry flags (--no-mixed,…
原文语言：英语
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 build, read-group injection, the collate/fixmate/sort/markdup…
原文语言：英语
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 reduces reference bias in the index itself, and whose MAPQ…
原文语言：英语
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, whose 255-for-unique MAPQ breaks GATK, and whose GeneCounts…
原文语言：英语
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. Use when FastQC shows adapter content climbing toward the 3' end, when…
原文语言：英语
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 verifyBamID2/NGSCheckMate/somalier). Use when suspecting…
原文语言：英语
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 dedup/UMI/merge, and HTML/JSON reports. Use when preprocessing bulk…
原文语言：英语
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. Use when reads have poor-quality tails, when an assembly or…
原文语言：英语
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 sequences, and adapter content. Use when performing initial QC on raw…
原文语言：英语
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 (TIN), and saturation - with RSeQC, Qualimap, RNA-SeQC, and…
原文语言：英语
Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected single-strand/duplex consensus reads with fgbio. Use when the library has UMIs and accurate molecule counting or below-sequencer-floor error…
原文语言：英语