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Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying...
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.
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 call...
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter...
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 t...
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits.
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolvin...
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 ar...
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers.
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.
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted...
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types.
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.
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorop...
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions, visualize genetic structure, and choose optimal K for admixture...
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences.
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across sampl...
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...
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
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, es...
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation 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.
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