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
GPTomics AI Skills
GitHub ↗Browse published AI skills maintained by GPTomics. Compare skill descriptions and follow each source repository for setup instructions.
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269Repository stars across indexed skills
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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
GitHub
bio-microbiome-diversity-analysis
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...
☆ 300View skill
GitHub
bio-chipseq-qc
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...
☆ 300View skill
GitHub
bio-rna-quantification-count-matrix-qc
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
☆ 300View skill
GitHub
bio-longread-structural-variants
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...
☆ 300View skill
GitHub
bio-alignment-io
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...
☆ 300View skill
GitHub
bio-single-cell-scatac-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.
☆ 300View skill
GitHub
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.
☆ 300View skill
GitHub
bio-pileup-generation
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
☆ 300View skill
GitHub
bio-read-qc-quality-filtering
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have...
☆ 300View skill
GitHub
bio-variant-calling-joint-calling
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
☆ 300View skill
GitHub
bio-phylo-tree-manipulation
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use for rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, and extracting subtrees.
☆ 300View skill
GitHub
bio-atac-seq-footprinting
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 c...
☆ 300View skill
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