mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- - 第 14 页

bio-long-read-sequencing-nanopore-methylation

Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.

原文语言：英语

bio-longread-structural-variants

Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.

原文语言：英语

bio-metagenomics-abundance

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.

原文语言：英语

bio-metagenomics-amr-detection

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

原文语言：英语

bio-metagenomics-functional-profiling

Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.

原文语言：英语

bio-metagenomics-kraken

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.

原文语言：英语

bio-metagenomics-visualization

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic…

原文语言：英语

bio-metagenomics-metaphlan

Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with…

原文语言：英语

bio-metagenomics-strain-tracking

Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain…

原文语言：英语

bio-phasing-imputation-genotype-imputation

Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.

原文语言：英语

bio-phasing-imputation-haplotype-phasing

Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.

原文语言：英语

bio-phasing-imputation-imputation-qc

Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputation accuracy before GWAS.

原文语言：英语

bio-phasing-imputation-reference-panels

Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.

原文语言：英语

bio-single-cell-batch-integration

Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences. Use when integrating multiple scRNA-seq batches or datasets.

原文语言：英语

bio-single-cell-cell-annotation

Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.

原文语言：英语

bio-single-cell-cell-communication

Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when inferring ligand-receptor interactions between cell types.

原文语言：英语

bio-single-cell-data-io

Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading,…

原文语言：英语

bio-single-cell-doublet-detection

Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying…

原文语言：英语

bio-single-cell-lineage-tracing

Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectories.

原文语言：英语

bio-single-cell-markers-annotation

Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for differential expression between clusters, identifying cluster-specific markers, scoring gene sets, and assigning cell type labels. Use when finding…

原文语言：英语

bio-single-cell-metabolite-communication

Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict metabolite secretion and sensing patterns from scRNA-seq data. Use when studying metabolic crosstalk between cell populations or…

原文语言：英语

bio-single-cell-multimodal-integration

Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC. Use when analyzing CITE-seq, Multiome, or other multi-modal single-cell data.

原文语言：英语

bio-single-cell-perturb-seq

Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.

原文语言：英语

bio-single-cell-preprocessing

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 variable genes, and scaling data. Use when filtering,…

原文语言：英语

bio-single-cell-scatac-analysis

Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensionality reduction, clustering, peak calling, and motif activity scoring with chromVAR. Use when analyzing single-cell ATAC-seq data.

原文语言：英语

bio-single-cell-trajectory-inference

Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis. Use when inferring developmental trajectories or pseudotime.

原文语言：英语

bio-single-cell-clustering

Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE embeddings, and visualizing clusters. Use when…

原文语言：英语

bio-spatial-transcriptomics-image-analysis

Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.

原文语言：英语

bio-spatial-transcriptomics-spatial-communication

Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks. Use when analyzing cell-cell communication in…

原文语言：英语

bio-spatial-transcriptomics-spatial-data-io

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other…

原文语言：英语

bio-spatial-transcriptomics-spatial-deconvolution

Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type proportions from scRNA-seq references. Use when estimating cell type composition in spatial…

原文语言：英语

bio-spatial-transcriptomics-spatial-domains

Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions.

原文语言：英语

bio-spatial-transcriptomics-spatial-multiomics

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.

原文语言：英语

bio-spatial-transcriptomics-spatial-neighbors

Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.

原文语言：英语

bio-spatial-transcriptomics-spatial-preprocessing

Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data.

原文语言：英语

bio-spatial-transcriptomics-spatial-proteomics

Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with…

原文语言：英语

bio-spatial-transcriptomics-spatial-statistics

Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment. Use when computing spatial autocorrelation or co-occurrence statistics.

原文语言：英语

bio-spatial-transcriptomics-spatial-visualization

Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.

原文语言：英语

bio-variant-calling-clinical-interpretation

Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.

原文语言：英语

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

原文语言：英语