Browse Tools

Use this skill for Conda package and environment management in reproducible bioinformatics workflows. Covers conda create/install/update/remove, conda env YAML lifecycle, channel configuration, strict

Use when working with the R package cowplot for assembling publication-ready multi-panel figures from ggplot2 plots, applying clean publication themes, or saving plots with precise dimensions. cowplot

coxph — Cox Proportional Hazards Regression via R's survival package. Fits semiparametric Cox models with coxph(), creates survival objects with Surv(), estimates survival curves with survfit(), tests

Use when working with CPA, Compositional Perturbation Autoencoder, single-cell perturbation modeling, drug-response latent spaces, out-of-distribution prediction for unseen drug combinations, dose-res

Performs genetic differentiation analysis between populations using indices like Gst and Jost's D. Calculates p-values and confidence intervals using bootstrapping. Primarily used for population genet

DGL-LifeSci — deep graph learning toolkit for molecular property prediction, drug-target interaction (DTI), and reaction prediction. Converts SMILES strings to DGL molecular graphs, then applies GNN a

DMU skill for multivariate mixed-model analyses in animal breeding and veterinary genomics. Use this skill when users ask about DMU driver files, dmu1 plus dmuai/dmu4/dmu5/rjmc module selection, AI-RE

Interactive HTML tables in R via the DT package, which wraps the DataTables JavaScript library. Use this skill for sortable/filterable/paginated tables, in-notebook display of large data frames, colum

Use when working with eDNAFlow, the Nextflow plus Singularity workflow for environmental DNA processing from raw single-end or paired-end FASTQ through quality filtering, demultiplexing, ZOTU generati

EEMS (Estimating Effective Migration Surfaces) infers spatial population structure by estimating effective migration and diversity rates on a triangular grid of demes using MCMC. Use for visualizing b

ENCODE tools provide access to the Encyclopedia of DNA Elements data, including genomic functional elements, ChIP-seq, RNA-seq, and ATAC-seq data. Facilitates data retrieval, query, and analysis for e

EnhancedVolcano — R/Bioconductor package for creating publication-ready volcano plots with enhanced colouring and labeling from differential expression results. Visualize DESeq2, limma, edgeR output w

Use this skill for ENMeval workflows in R when you need ecological niche model tuning, cross-validation partitioning, model selection, and null-model significance tests for species distribution modeli

Enrichr — web-based gene set enrichment analysis platform providing instant over-representation analysis against ~300 gene set libraries containing ~400,000 annotated gene sets. Implements Fisher's ex

Use when working with Entrez Direct (EDirect), NCBI's Unix command-line toolkit for E-utilities queries, linked-record traversal, filtered retrieval, XML extraction, local archive workflows, and scrip

Use this skill for Eugene, the rule-based language and software framework for specifying and constraining synthetic biological parts, devices, and systems. Covers Eugene language syntax (Part, Device,

Use when working with exactextractr, the R package for fast and accurate zonal statistics from raster data over polygon features. Supports `exact_extract` for named and custom summaries, weighted stat

Expression Atlas is the EMBL-EBI database and programmatic toolkit for querying baseline and differential gene expression across thousands of experiments in 50+ species. Use this skill to search exper

FactoMineR — R package for multivariate exploratory data analysis providing principal component analysis (PCA), correspondence analysis (CA), multiple correspondence analysis (MCA), multiple factor an

Use when working with FieldTrip for MEG, EEG, and iEEG analysis in MATLAB. Covers event definition, preprocessing, visual artifact rejection, ICA cleanup, time-locked ERF/ERP analysis, time-frequency

flashier — CRAN R package for Empirical Bayes Matrix Factorization (EBMF). Decomposes a data matrix Y ≈ LF' + E by placing adaptive empirical Bayes priors on loadings (L) and factors (F) via the ebnm

Use when working with flowCore — the foundational Bioconductor R package for reading, writing, and manipulating flow cytometry FCS files. Provides core data structures (flowFrame, flowSet), compensati

FlowJo v10 skill for flow-cytometry and mass-cytometry analysis workflows. Use when users need compensation setup, gating hierarchy design, batch processing, statistics table export, plugin-assisted a

Use when working with flowWorkspace for hierarchical cytometry gating in R. Supports GatingSet and GatingHierarchy workflows, loading FCS data into cytoset/cytoframe backends, editing gates with gs_po

Forensic genetics — probabilistic genotyping, STR mixture interpretation, kinship and paternity analysis, population allele frequency databases, and NGS-based forensic sequencing. Covers R packages: f

Galaxy — open-source web-based platform for accessible, reproducible, and transparent computational biology. Provides a browser GUI and REST API for running bioinformatics tools without command-line e

Use when working with ganon (ganon2) for metagenomic read classification, taxonomic binning/profiling, large-scale reference database builds, or incremental database updates from RefSeq/GenBank/GTDB.

GAPIT (Genome Association and Prediction Integrated Tool) — R package for genome-wide association studies (GWAS) and genomic prediction. Implements GLM, MLM, CMLM, MLMM, FarmCPU, BLINK, and SUPER mode

Use when working with GEARS, the SNAP Stanford method for predicting transcriptional outcomes of single-gene and multi-gene perturbations from single-cell RNA-seq perturbation screens. GEARS exposes t

Geemap is a Python package for interactive geospatial analysis and visualization with Google Earth Engine. Use this skill for Earth Engine mapping in Jupyter, split-map comparisons, time sliders, data

gganimate — R package that extends ggplot2 with animation capabilities, enabling frame-by-frame transitions, reveals, and state changes in scientific visualizations. Produces animated GIFs, MP4 videos

ggbeeswarm extends ggplot2 with beeswarm and quasi-random scatter geoms for categorical data visualization in R. Use geom_beeswarm() for deterministic non-overlapping point layouts and geom_quasirando

ggrepel — R package that extends ggplot2 with geom_text_repel() and geom_label_repel() to automatically position non-overlapping text labels on scatter plots, volcano plots, MA plots, PCA/UMAP plots,

ggthemes — R package extending ggplot2 with publication-quality themes, scales, and geoms inspired by well-known data visualizations (The Economist, FiveThirtyEight, Wall Street Journal, Stata, Tablea

Git LFS (Large File Storage) for repositories that must version large binary assets such as sequencing archives, imaging tiles, trained model weights, and reference bundles without bloating normal Git

The Google Earth Engine Python API allows developers to interact with Google Earth Engine, a cloud-based platform for planetary-scale geospatial analysis. It enables users to analyze and visualize sat

h5py — the standard Pythonic interface to HDF5 binary data format. Provides hierarchical storage for large numerical datasets with seamless NumPy integration. Supports compression (GZIP, LZF, SZIP), c

hapROH detects runs of homozygosity (ROH) in ancient and modern genomes using a Hidden Markov Model (HMM) that leverages a phased reference panel. Designed for low-coverage and pseudo-haploid ancient

hic2cool converts Juicer `.hic` contact matrices into Cooler `.cool` or multi-resolution `.mcool` files and supports normalization-vector migration and extraction. Use when users need hic-to-cool conv

hierfstat — CRAN R package for computing hierarchical F-statistics and population genetics diversity metrics. Implements Weir and Cockerham's Fst, Nei's Gst, Dest (Jost's D), allelic richness, and boo

Use when working with HistoQC for digital pathology slide quality control, whole-slide image artifact screening, and cohort-level WSI QC triage. HistoQC runs configurable module pipelines on SVS and r

Use when users mention holoviews, HoloViews, hv, declarative plotting in Python, backend-agnostic visualization, or interactive scientific plots in Jupyter. HoloViews represents data as Elements and C

Use when working with HoVer-Net for simultaneous nuclei instance segmentation and nuclei-type classification in H&E histology images. Covers official PyTorch training and inference flows from vqdang/h

HPO tools — query, annotate, and compare phenotypes using the Human Phenotype Ontology (HPO). Supports term lookup by HP ID or free text, semantic similarity scoring (Resnik, Lin, Jiang-Conrath), gene

Hugging Face Transformers — state-of-the-art machine learning library for natural language processing, computer vision, audio, and multimodal tasks. Provides pretrained models (BERT, GPT-2, T5, Llama,

igraph — Fast, open-source C library with Python, R, and Mathematica interfaces for graph and network analysis. Used in biological network analysis, protein-protein interaction (PPI) networks, gene re

IHW — Independent Hypothesis Weighting for covariate-informed multiple testing correction with increased statistical power. Accepts p-values and an independent covariate, learns data-driven weights vi

immunarch — R package for fast, painless analysis of immune repertoires from TCR and BCR sequencing data. Loads repertoire files from 10x Genomics, AIRR/IMGT, MiXCR, VDJtools, ImmunoSEQ, and other for

ImmuneBuilder — deep-learning models for predicting 3D structures of immune proteins from amino acid sequence alone. Provides three specialist predictors: ABodyBuilder2 (paired antibody Fv), NanoBodyB

IQ-TREE ModelFinder routing skill for maximum-likelihood phylogenetic model selection, partition merging, and reproducible tree inference from aligned DNA, amino-acid, codon, binary, morphological, an