Best bioinformatics skills, page 16

Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene).

jaechang-hits/SciAgent-Skills

Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots.

jaechang-hits/SciAgent-Skills

Unified biological database evidence owner. An agent skill from foryourhealth111-pixel/Vibe-Skills.

foryourhealth111-pixel/Vibe-Skills

Primary retained Python toolkit for molecular biology sequence work.

foryourhealth111-pixel/Vibe-Skills

Bioinformatics literature analysis workflow extraction and customized plan design.

aipoch/medical-research-skills

NGS analysis toolkit. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Access ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data.

aipoch/medical-research-skills

A skill your agent uses when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems.

aipoch/medical-research-skills

A skill your agent uses when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart.

aipoch/medical-research-skills

Standard single-cell RNA-seq analysis pipeline. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index…

exon-research/genomi

Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.

exon-research/genomi

Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.

exon-research/genomi

Analyzes base-editing screens for variant function. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for…

GPTomics/bioSkills

Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier…

GPTomics/bioSkills

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework.

GPTomics/bioSkills

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure.

GPTomics/bioSkills

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via…

GPTomics/bioSkills

Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired…

GPTomics/bioSkills

Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via…

GPTomics/bioSkills

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer…

GPTomics/bioSkills

Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP…

GPTomics/bioSkills

Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI…

GPTomics/bioSkills

Assigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom…

GPTomics/bioSkills

Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number Re, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2…

GPTomics/bioSkills

Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV…

GPTomics/bioSkills

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice)…

GPTomics/bioSkills

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel…

GPTomics/bioSkills

Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal).

GPTomics/bioSkills

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking…

GPTomics/bioSkills

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools…

GPTomics/bioSkills

Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS.

GPTomics/bioSkills

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML.

GPTomics/bioSkills

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

GPTomics/bioSkills

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX…

GPTomics/bioSkills

Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence).

GPTomics/bioSkills

Nominates and assesses CRISPR off-target sites genome-wide. An agent skill from GPTomics/bioSkills.

GPTomics/bioSkills

Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model.

GPTomics/bioSkills

Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismarkmethylationextractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the…

GPTomics/bioSkills

Tests individual CpG sites for differential methylation (DMC/DMP) from bisulfite sequencing counts or array/continuous beta-value matrices.

GPTomics/bioSkills

Detects differentially methylated regions (DMRs) from short-read bisulfite (WGBS/RRBS), array, and long-read methylation count tables using dmrseq (permutation region-FDR over the region selection)…

GPTomics/bioSkills

Designs and defends an epigenome-wide association study (EWAS) on 450K/EPIC array or bisulfite methylation - the layer deciding whether a hit is credible.

GPTomics/bioSkills

Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removing primers with cutadapt (--discard-untrimmed), learning a per-run error model…

GPTomics/bioSkills

Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative), ANCOM-BC2/ANCOMBC…

GPTomics/bioSkills

Alpha and beta diversity of an amplicon (16S/ITS) ASV/OTU community table - observed features, Shannon, Pielou evenness, Faith PD, Bray-Curtis, Jaccard, weighted/unweighted/generalized UniFrac…

GPTomics/bioSkills

Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic interpolation of reference-genome gene content - EPA-ng placement, gappa, castor…

GPTomics/bioSkills

Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality]…

GPTomics/bioSkills