GPTomics AI Skills

Browse published AI skills maintained by GPTomics. Compare skill descriptions and follow each source repository for setup instructions.

Author statistics

Indexed skills

269

Repository stars across indexed skills

80,661

Repository forks

13,719

Average repository stars per indexed skill

300

Repository stars may repeat across skills from the same repository.

Popular categories

Recent indexing activity

GitHub

bio-filter-sequences

GPTomics

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.

☆ 300View skill

GitHub

bio-genome-assembly-short-read-assembly

GPTomics

De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes.

☆ 300View skill

GitHub

bio-restriction-enzyme-selection

GPTomics

Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning.

☆ 300View skill

GitHub

bio-metabolomics-normalization-qc

GPTomics

Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before st...

☆ 300View skill

GitHub

bio-imaging-mass-cytometry-phenotyping

GPTomics

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker e...

☆ 300View skill

GitHub

bio-population-genetics-plink-basics

GPTomics

PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 a...

☆ 300View skill

GitHub

bio-hi-c-analysis-matrix-operations

GPTomics

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices.

☆ 300View skill

GitHub

bio-seq-objects

GPTomics

Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.

☆ 300View skill

GitHub

bio-reporting-rmarkdown-reports

GPTomics

Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.

☆ 299View skill

GitHub

bio-reporting-quarto-reports

GPTomics

Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.

☆ 299View skill

GitHub

bio-data-visualization-color-palettes

GPTomics

Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.

☆ 299View skill

GitHub

bio-entrez-link

GPTomics

Find cross-references between NCBI databases using Biopython Bio.Entrez. Use for navigating from genes to proteins, sequences to publications, finding related records, and discovering database relationships.

☆ 299View skill

GitHub

bio-entrez-fetch

GPTomics

Retrieve records from NCBI databases using Biopython Bio.Entrez. Use for downloading sequences, fetching GenBank records, getting document summaries, and parsing NCBI data into Biopython objects.

☆ 299View skill

GitHub

bio-entrez-search

GPTomics

Search NCBI databases using Biopython Bio.Entrez. Use for finding records by keyword, building search queries, discovering database structure, and getting global query counts across databases.

☆ 299View skill

GitHub

bio-structural-biology-alphafold-predictions

GPTomics

Access and analyze AlphaFold protein structure predictions. Use when you need predicted structures for proteins without experimental structures, or confidence scores (pLDDT).

☆ 299View skill

GitHub

bio-methylation-methylkit

GPTomics

DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comp...

☆ 299View skill

GitHub

bio-workflows-rnaseq-to-de

GPTomics

End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization.

☆ 299View skill

GitHub

bio-pathway-reactome

GPTomics

Reactome pathway enrichment using ReactomePA package. Performs over-representation analysis and GSEA on Reactome pathways, a curated peer-reviewed knowledgebase of biological pathways. Supports visualization an...

☆ 299View skill

GitHub

bio-atac-seq-differential-accessibility

GPTomics

Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq...

☆ 299View skill

GitHub

bio-proteomics-differential-abundance

GPTomics

Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes...

☆ 299View skill

GitHub

bio-geo-data

GPTomics

Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use for finding microarray/RNA-seq datasets, downloading expression data, and linking GEO to SRA.

☆ 299View skill

GitHub

bio-chipseq-peak-annotation

GPTomics

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation p...

☆ 299View skill

GitHub

bio-longread-alignment

GPTomics

Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant c...

☆ 299View skill

GitHub

bio-microbiome-qiime2-workflow

GPTomics

QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or workin...

☆ 299View skill

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.