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Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado or Guppy basecallers. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when proces...
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure.
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classe...
Modify protein structures using Biopython Bio.PDB. Use for transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, renumbering residues, and building stru...
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping.
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves a...
Parse and write protein structure files using Biopython Bio.PDB. Use for reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, extracting header information, and writing structures to variou...
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis...
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untarget...
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic...
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen cou...
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for...
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for u...
Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts.
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use to validate RNA-seq libraries before differential ex...
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt.
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or conv...
Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use after alignment to verify data quality before variant calling or qu...
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performan...
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks.
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calculating QC metrics, filtering cells and genes, normalizing counts, identifying highly vari...
默认按已收录数据中的 GitHub 仓库 Stars 排序。Stars 属于来源仓库，同一仓库的多个技能可能共享相同数值；它反映仓库关注度，不代表单个技能的安装量或质量评分。