GitHub
bio-restriction-mapping
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps.
☆ 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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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.
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GitHub
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,...
☆ 300View skill
GitHub
bio-blast-searches
Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use for sequence similarity searches, identifying unknown sequences, finding homologs, and querying NCBI's nr/nt databases.
☆ 300View skill
GitHub
bio-variant-calling-deepvariant
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
☆ 300View skill
GitHub
bio-population-genetics-scikit-allel-analysis
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structu...
☆ 300View skill
GitHub
bio-pdb-geometric-analysis
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use for measuring distances, angles, and dihedrals, finding neighbor atoms, superimposing structures, calculating RMSD, identifying...
☆ 300View skill
GitHub
bio-population-genetics-selection-statistics
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweep...
☆ 300View skill
GitHub
bio-de-edger-basics
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estim...
☆ 300View skill
GitHub
bio-primer-design-primer-validation
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability.
☆ 300View skill
GitHub
bio-hi-c-analysis-hic-data-io
Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats.
☆ 300View skill
GitHub
bio-sequence-properties
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
☆ 300View skill
GitHub
bio-genome-intervals-coverage-analysis
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencin...
☆ 300View skill
GitHub
bio-motif-search
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme a...
☆ 300View skill
GitHub
bio-spatial-transcriptomics-spatial-data-io
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates.
☆ 300View skill
GitHub
bio-basecalling
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado or Guppy basecallers. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when proces...
☆ 300View skill
GitHub
bio-hi-c-analysis-tad-detection
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure.
☆ 300View skill
GitHub
bio-metabolomics-lipidomics
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classe...
☆ 300View skill
GitHub
bio-pdb-structure-modification
Modify protein structures using Biopython Bio.PDB. Use for transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, renumbering residues, and building stru...
☆ 300View skill
GitHub
bio-workflows-metabolomics-pipeline
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping.
☆ 300View skill
GitHub
bio-metabolomics-targeted-analysis
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves a...
☆ 300View skill
GitHub
bio-pdb-structure-io
Parse and write protein structure files using Biopython Bio.PDB. Use for reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, extracting header information, and writing structures to variou...
☆ 300View skill
GitHub
bio-metabolomics-msdial-preprocessing
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis...
☆ 300View skill
GitHub
bio-metabolomics-metabolite-annotation
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untarget...
☆ 300View skill
GitHub
bio-proteomics-ptm-analysis
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic...
☆ 300View 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.