GitHub
bio-alignment-filtering
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
☆ 300View skill
tools bioinformatics AI Skills
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GitHub
bio-reference-operations
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
☆ 300View skill
GitHub
bio-imc-interactive-annotation
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training c...
☆ 300View skill
GitHub
bio-workflows-chipseq-pipeline
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
☆ 300View skill
GitHub
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.
☆ 300View skill
GitHub
bio-methylation-dmr-detection
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions o...
☆ 300View skill
GitHub
bio-flow-cytometry-cytometry-qc
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...
☆ 300View skill
GitHub
bio-expression-matrix-sparse-handling
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.
☆ 300View skill
GitHub
bio-copy-number-gatk-cnv
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...
☆ 300View skill
GitHub
bio-multi-omics-similarity-network
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
☆ 300View skill
GitHub
bio-genome-intervals-proximity-operations
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...
☆ 300View skill
GitHub
bio-chip-seq-super-enhancers
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...
☆ 300View skill
GitHub
bio-workflows-gwas-pipeline
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.
☆ 300View skill
GitHub
bio-genome-assembly-metagenome-assembly
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...
☆ 300View skill
GitHub
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 ar...
☆ 300View skill
GitHub
bio-variant-calling-structural-variant-calling
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.
☆ 300View skill
GitHub
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.
☆ 300View skill
GitHub
bio-methylation-bismark-alignment
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...
☆ 300View skill
GitHub
bio-multi-omics-data-harmonization
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types.
☆ 300View skill
GitHub
bio-compressed-files
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.
☆ 300View skill
GitHub
bio-flow-cytometry-compensation-transformation
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorop...
☆ 300View skill
GitHub
bio-population-genetics-population-structure
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...
☆ 300View skill
GitHub
bio-vcf-basics
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
☆ 300View skill
GitHub
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.
☆ 300View skill
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