В каталоге 183 730 навыков в 14 категориях.
Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-...
Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClea...
Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populati...
Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Cov...
Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF),...
Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and...
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file fo...
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new p...
Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corre...
Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding f...
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for...
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and fin...
Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using Dif...
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (...
Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, Ce...
Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict trans...
Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarg...
Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization),...
Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk...
Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species v...
Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evi...
Assigns GO terms, Pfam/InterPro domains, KEGG orthologs, EC numbers, and product names to predicted proteins using eggNO...
Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search again...
Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-complia...
Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family libra...
Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools...
Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), comp...
Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a sing...
Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with...
Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-on...
Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Ca...
Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHI...
Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap space...
Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (l...
Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activi...
Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas...
Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA...
Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance w...
Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (P...
Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the...
Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedt...
Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) w...
Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (wind...
Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon...
Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/...
Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test again...
Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest...
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when findi...
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray...
Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-nor...
Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked...
Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using coo...
Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare,...
Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-C,...
Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) w...
Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregate...
Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected wi...
Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation...
This skill should be used when the user needs to visualize BAM alignment files in IGV (Integrative Genomics Viewer). Tri...
Segment single cells from multiplexed IMC/MIBI tissue images using Mesmer/DeepCell, Cellpose, or ilastik+CellProfiler, c...
Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover com...
Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experim...
Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering...
Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-bas...
Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cel...
Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering...
Predict B-cell and T-cell epitopes for vaccine antigen design and epitope mapping with BepiPred-3.0, DiscoTope-3.0, the...
Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, B...
Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate c...
Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and Mi...
Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for pers...
Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and data...
Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath,...
Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt r...
Create a Linktree-style bio link hub page as a single self-contained HTML file. Triggers on: "create a bio link page", "...
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment...
Parse scholarly articles (PDF, DOI, URL) to extract metadata, GEO accessions, and acquisition links using OpenAlex + GRO...
Run BLAST searches locally using NCBI BLAST+ command-line tools.
Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, buildin...
Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.
Evaluates scientific research rigor using systematic frameworks. Assesses methodology, statistics, biases, and evidence...
Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accur...
Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage...
Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) wi...
Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxf...
Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-matched...
Assesses Oxford Nanopore and PacBio long-read quality with NanoPlot, cramino, NanoComp, pycoQC/toulligQC, and seqkit, an...
Polishes Oxford Nanopore draft assemblies to higher consensus accuracy with medaka, a basecaller-model-specific neural c...
Calls DNA base modifications (5mC, 5hmC, 6mA, 4mC) directly from Oxford Nanopore and PacBio HiFi long reads encoded as M...
Detects structural variants (deletions, insertions, inversions, duplications, translocations) from Oxford Nanopore and P...
Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RN...
Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitori...
Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI),...
Selects biomarker features from high-dimensional omics data using Boruta all-relevant selection, mRMR, LASSO/elastic-net...
Validates predictive models on omics and biomedical data with nested cross-validation, group/batch/temporal-aware splits...
Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random fore...
Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap,...
Builds and validates predictive time-to-event models on clinical and omics data with penalized Cox, random survival fore...
Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure...