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Writing & Content · By GPTomics
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants)… | GPTomics/ | 1.2k | 2 repos | ~7.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline… | GPTomics/ | 1.2k | 1 repo | ~3.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). | GPTomics/ | 1.2k | 1 repo | ~2k | Automated safety check: Pass | MIT | 1 mo ago |
| 4 | Detect and quantify translated ORFs from Ribo-seq using 3-nucleotide periodicity, including uORFs, internal ORFs, dORFs, and novel ORFs. | GPTomics/ | 1.2k | 1 repo | ~3.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | Preprocess ribosome profiling reads with UMI handling, adapter trimming, contaminant/rRNA depletion, and footprint-aware alignment. | GPTomics/ | 1.2k | 1 repo | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 6 | Validate Ribo-seq library quality by measuring 3-nucleotide periodicity and calibrating read-length-specific P-site offsets. | GPTomics/ | 1.2k | 1 repo | ~2.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 7 | Detect ribosome pausing and stalling at codon resolution from Ribo-seq, using local-relative occupancy metrics and A-site assignment. | GPTomics/ | 1.2k | 1 repo | ~3.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 8 | Quantify translation efficiency (TE) as ribosome occupancy relative to mRNA abundance and test for differential TE between conditions. | GPTomics/ | 1.2k | 1 repo | ~2.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding. | GPTomics/ | 1.2k | 1 repo | ~3.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Orchestrates genome-scale metabolic modeling from a protein FASTA to flux predictions, chaining CarveMe/gapseq reconstruction, memote QC, gap-filling, media-constrained FBA/FVA, gene essentiality… | GPTomics/ | 1.2k | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation efficiency, and stalling. | GPTomics/ | 1.2k | 1 repo | ~2.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 12 | Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes… | GPTomics/ | 1.2k | 1 repo | ~6.9k | Automated safety check: Pass | MIT | 1 mo ago |
