Best bioinformatics skills, page 17

Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and primer region - DADA2 assignTaxonomy + addSpecies (RDP naive Bayes), DECIPHER IDTAXA…

GPTomics/bioSkills

Harmonizes already-normalized per-omic matrices onto a common footing before joint integration - assembling a MultiAssayExperiment, choosing the per-omic variance-stabilizing transform, deciding…

GPTomics/bioSkills

Chooses a bulk multi-omics integration strategy before any tool runs by mapping the biological question (subtype discovery, shared axis of variation, predictive signature, pairwise correlation) to a…

GPTomics/bioSkills

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/bioSkills

Estimate divergence times under molecular-clock models with BEAST2, MCMCTree/PAML, TreePL, and LSD2, framing a date as a product of the calibration prior and the clock model far more than of the…

GPTomics/bioSkills

Infers maximum-likelihood phylogenetic trees with IQ-TREE2 and RAxML-NG -- model selection (ModelFinder), branch support (UFBoot2, SH-aLRT), concordance factors (gCF/sCF), partitioning, topology…

GPTomics/bioSkills

Estimates species trees under the multispecies coalescent from per-locus gene trees with the modern ASTER astral binary (ASTRAL-III/wASTRAL/ASTRAL-Pro), plus SVDQuartets, BPP, and StarBEAST2.

GPTomics/bioSkills

Scans genomes for natural selection with SFS tests (Tajima's D, Fay & Wu H, Zeng E, SweepFinder2 CLR), haplotype tests (iHS, nSL, XP-EHH, Rsb, H12), and differentiation (FST, PBS) using…

GPTomics/bioSkills

Designs and ranks PCR primer pairs for a target template with primer3-py (designprimers), returning pairs with nearest-neighbor Tm, GC, product size, and complementarity scores.

GPTomics/bioSkills

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/bioSkills

Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives.

GPTomics/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

Clusters temporally variable genes by expression-profile SHAPE (not significance) using Mfuzz fuzzy c-means, TCseq, DEGreport degPatterns, and tslearn DTW/soft-DTW.

GPTomics/bioSkills

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/bioSkills

Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR.

GPTomics/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

View, query, and interpret VCF/BCF variant files with bcftools and cyvcf2.

GPTomics/bioSkills

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes.

GPTomics/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

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/bioSkills

Orchestrates genomic-epidemiology outbreak investigation from pathogen isolates to transmission networks, forking bacterial (snippy - Gubbins recombination-masking - IQ-TREE - TreeTime - TransPhylo)…

GPTomics/bioSkills

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment.

GPTomics/bioSkills

Variant and VCF workflow guide for local SNV, indel, and structural-variant summarization, filtering, and consequence triage.

DrugClaw/DrugClaw

Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events.

TianGzlab/OmicsClaw

Fit SimBiology model parameters to data — fitproblem, population NLME, virtual patients, and NCA.

matlab/matlab-agentic-toolkit

Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.

FreedomIntelligence/OpenClaw-Medical-Skills

scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference.

jaechang-hits/SciAgent-Skills

Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit.

aiskillstore/marketplace

Deep generative models for single-cell omics; use when you need probabilistic batch correction (scVI), transfer learning, uncertainty-aware differential expression, or multimodal integration…

aipoch/medical-research-skills

Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

aipoch/medical-research-skills

A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

aipoch/medical-research-skills

Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis…

aipoch/medical-research-skills

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment…

aipoch/medical-research-skills

Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

aipoch/medical-research-skills

Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence…

aipoch/medical-research-skills

Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

aipoch/medical-research-skills

Designs complete integrated research plans for bulk transcriptomics, proteomics, metabolomics, and related omics from a user-provided biomedical direction.

aipoch/medical-research-skills

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

aipoch/medical-research-skills

Generates complete dual-disease transcriptomic + machine learning research designs from a user-provided disease pair.

aipoch/medical-research-skills