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SkillsMP a collecté 496 skills depuis zja2004/BGI-CLI. Ouvrez un skill pour examiner sa source et ses détails.
zja2004/BGI-CLIAffichage de 40 skills collectés sur 496.
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when…
Langue du texte source : anglais
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing…
Langue du texte source : anglais
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when…
Langue du texte source : anglais
Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting…
Langue du texte source : anglais
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma…
Langue du texte source : anglais
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between…
Langue du texte source : anglais
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
Langue du texte source : anglais
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq…
Langue du texte source : anglais
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use…
Langue du texte source : anglais
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream…
Langue du texte source : anglais
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.
Langue du texte source : anglais
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
Langue du texte source : anglais
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
Langue du texte source : anglais
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
Langue du texte source : anglais
Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.
Langue du texte source : anglais
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
Langue du texte source : anglais
Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.
Langue du texte source : anglais
Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.
Langue du texte source : anglais
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
Langue du texte source : anglais
Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.
Langue du texte source : anglais
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
Langue du texte source : anglais
Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
Langue du texte source : anglais
Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
Langue du texte source : anglais
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
Langue du texte source : anglais
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
Langue du texte source : anglais
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.
Langue du texte source : anglais
Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.
Langue du texte source : anglais
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.
Langue du texte source : anglais
Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying CRISPR base editor results, comparing ABE vs CBE efficiency, or assessing prime editing fidelity.
Langue du texte source : anglais
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
Langue du texte source : anglais
CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use when analyzing amplicon sequencing data from CRISPR editing experiments to assess editing efficiency.
Langue du texte source : anglais
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 count data after QC passes.
Langue du texte source : anglais
JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.
Langue du texte source : anglais
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
Langue du texte source : anglais
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or…
Langue du texte source : anglais
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosing poor screen performance.
Langue du texte source : anglais
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor…
Langue du texte source : anglais
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis…
Langue du texte source : anglais
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when…
Langue du texte source : anglais
Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when…
Langue du texte source : anglais