В каталоге 183 730 навыков в 14 категориях.
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes...
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction,...
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove...
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter conte...
Runs RNA-seq-specific post-alignment QC - strandedness inference, gene-body 5'-3' coverage, read distribution (exonic/in...
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep...
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing seque...
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, ind...
Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence ident...
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using Mult...
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing...
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when gener...
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observ...
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML,...
Automatically handle molecular and cellular biology research about genes, proteins, variants, pathways, omics, cells, mo...
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce s...
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, si...
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sit...
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches...
Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASK...
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strand...
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use w...
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when pre...
Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing l...
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regul...
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Sal...
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effe...
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2...
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using txim...
Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rf...
Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAf...
Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts...
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage,...
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, con...
Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, c...
Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched mole...
Read/write FASTA, GenBank, FASTQ files. Sequence manipulation (complement, translate). Indexed random access via faidx....
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings,...
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use whe...
Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequence...
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzin...
Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (ele...
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints...
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variatio...
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for cons...
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor inter...
Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R). Resolve...
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PC...
Read, write, create, and convert single-cell objects across AnnData (Python), Seurat (R), and SingleCellExperiment (R)....
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data...
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python...
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics...
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for different...
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types....
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple mo...
Analyze Perturb-seq / CROP-seq single-cell CRISPR screens. Use when assigning guides as a mixture problem, removing non-...
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function thr...
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calc...
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensiona...
Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamental...
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for...
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific cons...
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data. Use when iden...
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miR...
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other smal...
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA tar...
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer inter...
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and Spatial...
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location,...
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots cons...
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay tria...
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics,...
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalizat...
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autoc...
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and...
Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context di...
Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring,...
Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audi...
Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TP...
Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Us...
Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, pref...
Aggregate results, train ML models, and produce reports with validated references.
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins withou...
Structure prediction and structure-based annotation.
Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS,...
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constra...
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy....
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Pred...
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generat...
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual cura...
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation fram...
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune...
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity pl...
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VD...
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analy...
Detects circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE,...
Discovers periodic signals of unknown period in time-series omics data using Lomb-Scargle periodograms (scipy), autocorr...
Clusters genes by temporal expression profile shape using Mfuzz soft clustering, TCseq, and DEGreport degPatterns. Group...