Browse Tools

Use this skill for SciTools Iris workflows on multidimensional Earth-science data: loading NetCDF/GRIB/PP into Cube objects, constraining and extracting subsets, aggregating over dimensions, regriddin

ISOLDE — interactive molecular dynamics plugin for UCSF ChimeraX that enables real-time model building into low-to-medium resolution cryo-EM and crystallographic maps. Uses GPU-accelerated OpenMM with

JAX — Google's high-performance numerical computing library combining NumPy API with automatic differentiation (grad, value_and_grad), just-in-time XLA compilation (jit), automatic vectorization (vmap

Laspy — Python library for reading, writing, and manipulating LAS and LAZ (compressed) LIDAR point cloud files conforming to ASPRS LAS specification versions 1.0 through 1.4. Supports chunked I/O for

LIANA (LIgand-receptor ANAlysis) — unified Python framework for cell-cell communication inference from single-cell transcriptomics. Wraps multiple methods (CellPhoneDB, NATMI, Connectome, SingleCellSi

Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut

MACS2 (Model-based Analysis of ChIP-Seq) — the standard peak caller for ChIP-seq and ATAC-seq experiments. Identifies transcription factor binding sites (narrow peaks), histone modification domains (b

MatchIt — R package for nonparametric preprocessing via propensity score matching in observational studies. Implements nearest neighbor, optimal, full, generalized full, genetic, exact, coarsened exac

MCIA (Multiple Co-Inertia Analysis) — R/Bioconductor omicade4 package for simultaneous dimensionality reduction across multiple paired omics datasets. Identifies co-structure axes (co-inertia) that ar

mediation — R package for causal mediation analysis implementing parametric and non-parametric methods. Core function mediate() estimates average causal mediation effects (ACME), average direct effect

methylclock — R/Bioconductor package for computing DNA methylation-based biological age estimates using epigenetic clocks. Implements Horvath (2013), Hannum (2013), Levine/PhenoAge (2018), Zhang (2019

MHCflurry — open-source Python package for MHC class I peptide binding affinity and antigen presentation prediction. Accepts peptide sequences (8-15 amino acids) and HLA allele names (e.g., HLA-A*02:0

Use when working with modelangelo — modelAngelo — automated atomic model

Use when working with mokapot — mokapot -- Python package for semi-supervised

Mowgli — multi-omics Wasserstein integrated analysis using group NMF to jointly factorize paired multi-omics data (RNA, ATAC, protein/ADT) from single-cell experiments. Learns shared and modality-spec

Use when assessing MRI image quality, extracting Image Quality Metrics (IQMs), running quality control on BIDS neuroimaging datasets, or generating QC reports for T1w, T2w, or BOLD fMRI data. Covers M

MSBooster — deep-learning rescoring tool for proteomics database search results. Predicts peptide retention time, ion mobility, and MS2 fragmentation spectra using models via Koina (Prosit, AlphaPeptD

MSIsensor2 detects microsatellite instability (MSI) in tumor-only sequencing data using machine learning — no paired normal sample required. Supports whole-exome sequencing (WES), whole-genome sequenc

NAMD — high-performance parallel molecular dynamics for large biomolecular systems. Runs on CPU clusters and GPUs with CHARMM and AMBER force fields. Supports explicit/implicit solvent, enhanced sampl

NeuralGCM — hybrid ML-physics atmospheric model for weather forecasting and climate simulation built on JAX and the Dinosaur spectral dynamical core. Provides PressureLevelModel API for loading pre-tr

nf-core/eager is a Nextflow pipeline for ancient DNA (aDNA) and palaeogenomics analysis. Handles adapter trimming, low-complexity filtering, read mapping with BWA-aln (optimal for short aDNA reads), d

NicheNet — R-based computational framework for studying intercellular communication from single-cell transcriptomics. Predicts which ligands expressed by sender cell types regulate target gene express

Nirvana — Clinical-grade genomic variant annotation tool by Illumina that processes VCF files and outputs structured JSON with transcript consequences, population frequencies, pathogenicity scores, an

nloptr — R interface to the NLopt nonlinear optimization library. Provides a common interface to 30+ optimization algorithms covering local and global search, gradient-based and derivative-free method

Noodles — Rust bioinformatics I/O library with specification-compliant

Nucleotide Transformer — DNA foundation models by InstaDeep and BioNTech for genomic sequence analysis. Pre-trained transformer models (50M to 2.5B parameters) on 3,202 diverse genomes generate embedd

Use when working with OmicsIntegrator or OmicsIntegrator2 — a network-based multi-omics data integration framework from the Fraenkel Lab (MIT). Applies the Prize-Collecting Steiner Forest (PCSF) algor

'Use when working with opencravat — openCRAVAT — open-source variant

OpenMM — high-performance molecular dynamics simulation toolkit with GPU acceleration via CUDA and OpenCL. Provides Python API for building custom simulations, force field support (AMBER, CHARMM, AMOE

pairtools — Command-line toolkit for processing Hi-C and chromosome conformation capture contact pairs in the Open2C ecosystem. Parses alignments (SAM/BAM) into .pairs format, sorts, deduplicates, fil

Palantir — pseudotime and cell fate probability analysis for single-cell RNA-seq data using Markov diffusion chains. Computes a continuous pseudotime ordering from a user-specified start cell and quan

Papermill — parameterize, execute, and analyze Jupyter notebooks from the command line or Python API. Enables reproducible notebook-based bioinformatics pipelines by injecting parameters into tagged c

PCAngsd — principal component analysis and population genetics inference from genotype likelihoods in low-depth sequencing data. Use when performing PCA on low-coverage WGS, ancient DNA, or pooled seq

Use when converting PDF pages to images with pdf2image, a Python wrapper around Poppler tools (pdftoppm/pdftocairo). Covers PDF-to-PNG/JPEG/TIFF conversion, page-range extraction, grayscale rendering,

Perturb-seq analysis tools including MIMOSCA (Multi-Input Multi-Output Single-Cell Analysis) for CRISPR perturbation screens with single-cell RNA-seq readout. Handles guide RNA assignment to cells, pe

Phenix — comprehensive macromolecular structure determination from X-ray crystallography, cryo-EM, and neutron diffraction data. Provides automated molecular replacement (Phaser), structure refinement

Prosit — deep learning framework for predicting MS2 fragment ion spectra and indexed retention times (iRT) from peptide sequences. Enables in silico spectral library generation for any organism and pr

ProteinMPNN — deep learning-based protein sequence design from backbone structures. Uses message passing neural networks to predict amino acid sequences that fold into a given 3D backbone. Supports fi

pslMap and pslFilter are UCSC Kent utility programs for manipulating PSL (BLAT alignment) files. pslMap remaps PSL alignments from one coordinate space to another using a chain or mapping PSL file — u

Use when working with PubMedBERT — a BERT model pretrained from scratch on PubMed abstracts — for biomedical NLP tasks including named entity recognition, relation extraction, question answering, and

Use when working with PyG (PyTorch Geometric) — the PyTorch-based library for deep learning on graphs and irregular data structures. Supports graph neural networks (GNNs) including GCN, GAT, GraphSAGE

PyMC — probabilistic programming framework for Bayesian statistical modeling in Python. Define models with intuitive syntax using pm.Model() context manager, specify priors (Normal, HalfNormal, HalfCa

PyStan — Python interface to Stan for Bayesian statistical modeling and high-performance inference. Compile Stan programs (stan.build), draw posterior samples via HMC-NUTS (model.sample), extract draw

pyteomics -- Python library for proteomics and mass spectrometry data analysis. Reads and writes mzML, mzXML, MGF, FASTA, pepXML, mzIdentML, and other standard formats. Provides mass calculations, pep

Use when users need to test bioinformatics workflows or pipelines with YAML definitions in pytest. Covers authoring `test*.yml` files, validating schema keys (`name`, `command`, `files`, `stdout`, `st

PyTorch — open-source deep learning framework for building and training neural networks in biology and life sciences. Provides tensor computation with GPU acceleration, automatic differentiation (auto

Use when working with RColorBrewer — an R package providing ColorBrewer palettes by Cynthia Brewer for cartography and data visualization. Offers three palette types: sequential (18 palettes), divergi

readr — tidyverse R package for reading rectangular text data: CSV, TSV, fixed-width, whitespace-delimited, and log files. Provides fast parsing with automatic type inference, explicit col_types speci

RELION — Bayesian approach to cryo-EM single-particle analysis for 3D structure determination of biological macromolecules. Provides motion correction, CTF estimation, particle picking (autopicking, L

Remora is an Oxford Nanopore Technologies (ONT) tool for modified base calling from nanopore sequencing data. Trains neural network models to detect base modifications (5mC, 5hmC, m6A, pseudouridine,