bio-batch-processing
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
☆2.85k repo stars⑂396 repo forks
Documents
Documents skills
Browse reusable Agent Skills, each with a clear purpose and practical guidance.
bio-cfdna-preprocessing
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 cfDNA sequencing data before downstream analysis.
☆2.85k repo stars⑂396 repo forks
Documents
bio-chipseq-visualization
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.
☆2.85k repo stars⑂396 repo forks
Documents
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.
☆2.85k repo stars⑂396 repo forks
Documents
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.
☆2.85k repo stars⑂396 repo forks
Documents
bio-copy-number-cnv-visualization
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.
☆2.85k repo stars⑂396 repo forks
Documents
bio-crispr-screens-batch-correction
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.
☆2.85k repo stars⑂396 repo forks
Documents
bio-crispr-screens-crispresso-editing
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.
☆2.85k repo stars⑂396 repo forks
Documents
bio-de-results
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 filtering and exporting DE analysis results.
☆2.85k repo stars⑂396 repo forks
Documents
bio-differential-expression-batch-correction
Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.
☆2.85k repo stars⑂396 repo forks
Documents