Browse published AI skills maintained by GPTomics. Compare skill descriptions and follow each source repository for setup instructions.
Indexed skills
269Repository stars across indexed skills
80,661Repository forks
13,719Average repository stars per indexed skill
300Repository stars may repeat across skills from the same repository.
Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations. Use when building zoomable, hoverable plots for data exploration or web dashboard...
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures.
Protein grouping and inference from peptide identifications. Handles shared peptides, protein groups, and protein-level FDR control using parsimony and probabilistic approaches.
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when you need to map IDs for pathway analysis or to match different data sources.
Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio...
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use for identifying orthologs, distant homologs, and protein family members when standard BLA...
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats inc...
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use for comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DN...
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Tests whether GO terms are enriched in a gene list compared to background. Supports all three ontologies (BP, MF, CC), multiple ID type...
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite...
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance.
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully reso...
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
Access UniProt protein database for sequences, annotations, and functional information. Use when you need protein data, GO terms, domain annotations, or protein-protein interactions.
Annotate CNVs with genes, pathways, and clinical significance. Use to interpret CNV calls and identify affected genes.
Build, manage, and search spectral libraries for proteomics. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, tra...
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.