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Research & Science · By GPTomics
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 433 | Analyzes data-independent acquisition (DIA) proteomics by scoring reconstructed fragment-chromatogram peak groups against a decoy null with DIA-NN (library-free directDIA, library-based, or… | GPTomics/ | 1.2k | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 434 | Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives. | GPTomics/ | 1.2k | 1 repo | ~5.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 435 | Peptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than a raw engine score (XCorr, hyperscore… | GPTomics/ | 1.2k | 1 repo | ~5.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 436 | Quality control for bottom-up proteomics across three levels -- instrument/raw-signal (mass accuracy, RT/iRT fit, FWHM, TIC vs injection time, % MS2 identified), identification/run (missed… | GPTomics/ | 1.2k | 1 repo | ~6.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 437 | Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with… | GPTomics/ | 1.2k | 1 repo | ~6.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 438 | Quantifies protein abundance from mass spectrometry using label-free (LFQ/MaxLFQ, DIA fragment-level), isobaric (TMT/iTRAQ reporter ions, MS2 vs SPS-MS3), and metabolic (SILAC) approaches, including… | GPTomics/ | 1.2k | 1 repo | ~5.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 439 | Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence with Bio.PDB. | GPTomics/ | 1.2k | 1 repo | ~5.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 440 | Tests and estimates rhythmicity at a PRE-SPECIFIED period (canonically 24h) in time-series omics using cosinor regression (CosinorPy), JTKCYCLE/ARSER/Lomb-Scargle meta-analysis (MetaCycle meta2d)… | GPTomics/ | 1.2k | 1 repo | ~5.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 441 | Discovers a periodic signal of UNKNOWN period in time-series omics data and puts a defensible significance on it, especially when sampling is IRREGULAR (dropped timepoints, pooled harvests) so… | GPTomics/ | 1.2k | 1 repo | ~5.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 442 | Clusters temporally variable genes by expression-profile SHAPE (not significance) using Mfuzz fuzzy c-means, TCseq, DEGreport degPatterns, and tslearn DTW/soft-DTW. | GPTomics/ | 1.2k | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 443 | Models continuous temporal trajectories from BULK or time-resolved omics where the x-axis is measured experimental time: penalized GAMs (mgcv) for smooth trends and changepoint detection (segmented… | GPTomics/ | 1.2k | 1 repo | ~5.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 444 | Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR. | GPTomics/ | 1.2k | 1 repo | ~6.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 445 | Classify variant clinical significance with the ACMG/AMP germline framework and its 2018-2025 ClinGen refinements (graded PVS1 decision tree, PM2 downgraded to Supporting, PP5/BP6 retired… | GPTomics/ | 1.2k | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 446 | Joint genotype a cohort of per-sample gVCFs with GATK (HaplotypeCaller -ERC GVCF - GenomicsDBImport or CombineGVCFs - GenotypeGVCFs) or GLnexus for DeepVariant gVCFs, producing a squared-off… | GPTomics/ | 1.2k | 1 repo | ~6.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 447 | Call structural variants (=50 bp deletions, insertions, inversions, duplications, translocations) from short- or long-read data by reconstructing four orthogonal signals (discordant pairs, split… | GPTomics/ | 1.2k | 1 repo | ~7.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 448 | 448.Bio Vcf Basics View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2. | GPTomics/ | 1.2k | 1 repo | ~5.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 449 | End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. | GPTomics/ | 1.2k | 1 repo | ~5.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 450 | Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling… | GPTomics/ | 1.2k | 1 repo | ~6.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 451 | Orchestrates genome annotation from assembled contigs to functional annotation, forking prokaryotic (Bakta one-step, genetic-code table from GTDB-Tk) vs eukaryotic (RepeatMask - BRAKER3 - functional… | GPTomics/ | 1.2k | 1 repo | ~5.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 452 | Orchestrates gene regulatory network inference from processed single-cell data to regulons and in-silico perturbation, via pySCENIC (RNA-only GRNBoost2 - cisTarget - AUCell), SCENIC+ (multiome… | GPTomics/ | 1.2k | 1 repo | ~5.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 453 | End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference… | GPTomics/ | 1.2k | 1 repo | ~6.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 454 | Orchestrates VERTICAL bulk multi-omics integration (RNA + protein + methylation on the SAME samples) from harmonization to a validated result, routing to MOFA2 (shared factors), mixOmics/DIABLO… | GPTomics/ | 1.2k | 1 repo | ~5.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 455 | Orchestrates genomic-epidemiology outbreak investigation from pathogen isolates to transmission networks, forking bacterial (snippy - Gubbins recombination-masking - IQ-TREE - TreeTime - TransPhylo)… | GPTomics/ | 1.2k | 1 repo | ~6.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 456 | End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. | GPTomics/ | 1.2k | 1 repo | ~6k | Automated safety check: Pass | MIT | 1 mo ago |
| 457 | Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input… | GPTomics/ | 1.2k | 1 repo | ~4.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 458 | Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, HGDP+1kGP/gnomAD, CAAPA), matching panel ancestry to the target, reconciling… | GPTomics/ | 1.2k | 1 repo | ~4.4k | Automated safety check: Pass | MIT | 1 mo ago |
