Menü
Skills in diesem Repository
SkillsMP hat 562 Skills aus GPTomics/bioSkills gesammelt. Öffne einen Skill, um Quelle und Details zu prüfen.
GPTomics/bioSkillsEs werden 40 von 562 gesammelten Skills angezeigt.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Searches single enzymes, batches, or commercial enzyme sets and returns cut positions for linear or circular DNA. Use when locating where one or more restriction enzymes cut a…
Quellsprache: Englisch
Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one interactive MultiQC report, and guides module scoping, sample-name resolution, large-cohort behavior, and turning the report into an actual QC…
Quellsprache: Englisch
Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2. Use when preparing figures for journal submission, exporting a…
Quellsprache: Englisch
Runs parameterized Jupyter notebooks as reproducible batch report generators with papermill, renders them to HTML/PDF with nbconvert, aggregates results across samples, and makes notebook outputs trustworthy. Use when generating per-sample analysis reports,…
Quellsprache: Englisch
Builds publication-ready tables - descriptive Table 1, regression and differential-expression result tables, and supplementary tables - with gtsummary, gt, flextable, and kableExtra (R) or great_tables, pandas, and tableone (Python), choosing the right…
Quellsprache: Englisch
Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine selection, cache-vs-freeze semantics, native cross-references, parameters, and environment pinning. Use when creating a Quarto report of an…
Quellsprache: Englisch
Creates reproducible R Markdown analysis reports (HTML, PDF, Word) with knitr, covering the render pipeline, the interactive-vs-knit session trap, cache invalidation, bookdown cross-references, parameterization, and environment pinning. Use when generating an…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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, gseaplot2, and upsetplot. Covers why a default top-20 GO dotplot is…
Quellsprache: Englisch
Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE). Covers why the BACKGROUND universe (not the gene list) is the null and…
Quellsprache: Englisch
Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterProfiler's gseGO, gseKEGG, gsePathway, and GSEA (fgseaMultilevel engine), and scores per-sample pathway activity with ssGSEA and GSVA. Covers…
Quellsprache: Englisch
Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-reviewed, reaction-level pathways using ReactomePA's enrichPathway (ORA) and gsePathway (GSEA), reading the local reactome.db so a run is…
Quellsprache: Englisch
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,…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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,…
Quellsprache: Englisch
Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas9, NNGRRT SaCas9, TTTV Cas12a, NG SpCas9-NG, near-PAMless SpRY), enumerating candidate spacers, applying hard filters (Pol-III TTTT…
Quellsprache: Englisch
Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed)…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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)…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch
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…
Quellsprache: Englisch