GitHub
bio-variant-normalization
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
☆ 300View skill
tools bioinformatics AI Skills
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GitHub
bio-microbiome-amplicon-processing
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplic...
☆ 300View skill
GitHub
bio-workflows-microbiome-pipeline
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2.
☆ 300View skill
GitHub
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 abu...
☆ 300View skill
GitHub
bio-genome-intervals-interval-arithmetic
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent...
☆ 300View skill
GitHub
bio-alignment-indexing
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
☆ 300View skill
GitHub
bio-read-alignment-bowtie2-alignment
Align short reads using Bowtie2 with local or end-to-end modes. Use for ChIP-seq, ATAC-seq, or when you need flexible alignment modes. Supports gapped alignment.
☆ 300View skill
GitHub
bio-microbiome-taxonomy-assignment
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DAD...
☆ 300View skill
GitHub
bio-atac-seq-nucleosome-positioning
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing...
☆ 300View skill
GitHub
bio-differential-expression-timeseries-de
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns.
☆ 300View skill
GitHub
bio-proteomics-proteomics-qc
Quality control and assessment for proteomics data. Covers sample quality metrics, missing value patterns, replicate correlation, batch effect detection, and intensity distribution checks.
☆ 300View skill
GitHub
bio-crispr-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...
☆ 300View skill
GitHub
bio-workflows-atacseq-pipeline
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting.
☆ 300View skill
GitHub
bio-multi-omics-mixomics-analysis
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis.
☆ 300View skill
GitHub
bio-population-genetics-association-testing
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result vi...
☆ 300View skill
GitHub
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 imputat...
☆ 300View skill
GitHub
bio-variant-calling
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
☆ 300View skill
GitHub
bio-workflows-multi-omics-pipeline
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and othe...
☆ 300View skill
GitHub
bio-rna-quantification-tximport-workflow
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
☆ 300View skill
GitHub
bio-flow-cytometry-clustering-phenotyping
Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without...
☆ 300View skill
GitHub
bio-alignment-statistics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
☆ 300View skill
GitHub
bio-longread-medaka
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore...
☆ 300View skill
GitHub
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 fo...
☆ 300View skill
GitHub
bio-read-qc-fastp-workflow
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast...
☆ 300View skill
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