Best bioinformatics skills, page 10

Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI…

GPTomics/bioSkills

Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB)…

GPTomics/bioSkills

Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch…

GPTomics/bioSkills

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups…

GPTomics/bioSkills

Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GETHOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs).

GPTomics/bioSkills

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks.

GPTomics/bioSkills

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization…

GPTomics/bioSkills

Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4…

GPTomics/bioSkills

Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGenfinder…

GPTomics/bioSkills

Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens.

GPTomics/bioSkills

Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial…

GPTomics/bioSkills

Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions.

GPTomics/bioSkills

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution.

GPTomics/bioSkills

Analyzes alternative splicing at single-cell resolution. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Assesses RNA-seq data quality specifically for alternative splicing analysis.

GPTomics/bioSkills

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free…

GPTomics/bioSkills

Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart…

GPTomics/bioSkills

the R package BioNAR, developed to step by step analysis of PPI network.

bioMate-AI/biomate-bioconductor-kb

Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo…

ClawBio/ClawBio

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation.

ClawBio/ClawBio

Genome, transcriptome, and protein completeness assessment via BUSCO v6.

ClawBio/ClawBio

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the…

ClawBio/ClawBio

Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance…

ClawBio/ClawBio

Predict gene and transcript structure (intervals, exons, strand) from a DNA sequence using the Genomic Intelligence DNA Annotation model, via the hosted /v1/tasks/annotation/predict API.

ClawBio/ClawBio

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

ClawBio/ClawBio

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API.

ClawBio/ClawBio

Predict tissue / cell-type expression (log TPM + TPM) from 9,198–500,000 bp of DNA around a TSS, at least 4,599 bp each side (anything but exactly 9,198 bp needs --tss-index) using the Genomic…

ClawBio/ClawBio

Detect promoter regions in DNA sequences using the Genomic Intelligence G0 transformer (GENA-LM BERT Large), via the hosted /v1/tasks/promoter/predict API.

ClawBio/ClawBio

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API.

ClawBio/ClawBio

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).

ClawBio/ClawBio

End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.

ClawBio/ClawBio

Analyse 10x Visium spatial transcriptomics: SpaceRanger outs or spatial h5ad in, then QC, Leiden clustering, Wilcoxon markers, Moran's I, neighbourhood enrichment and co-occurrence in one local…

ClawBio/ClawBio

Query metadata and download data from the NCBI Gene Expression Omnibus (GEO).

ClawBio/ClawBio

Query metadata and download data from the PRIDE Archive, EMBL-EBI's proteomics identifications database, via the PRIDE Archive REST API v3.

ClawBio/ClawBio

Stage 2 of the spatial transcriptomics workflow — normalize 10x Visium data and cluster spatial spots.

QING1105/ezST

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.

aipoch/medical-research-skills

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for…

aipoch/medical-research-skills

Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis.

matlab/matlab-agentic-toolkit

Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq.

TianGzlab/OmicsClaw

Generates submission-ready Elsevier/SCI Highlights from manuscript text or extracted PDF/DOCX/TXT content.

aipoch/medical-research-skills

Infer gene regulatory networks (GRNs) from gene expression matrices using GRNBoost2 or GENIE3; use when analyzing bulk or single-cell RNA-seq to identify TF→target regulatory relationships.

aipoch/medical-research-skills

A skill your agent uses when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after…

aipoch/medical-research-skills

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores).

aipoch/medical-research-skills

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially…

aipoch/medical-research-skills

A skill your agent uses when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF…

aipoch/medical-research-skills

A skill your agent uses when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22 signature matrix…

aipoch/medical-research-skills

A skill your agent uses when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization.

aipoch/medical-research-skills

A skill your agent uses when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap.

aipoch/medical-research-skills