SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following publication By Sanborn MA et al in Nature Communications (2025…

An example on how to call the API of GPT4DFCI, a private and secure generative AI tool, based on GPT and o1 models and deployed for non-clinical use at Dana-Farber Cancer Institute.

Machine learning, in numpy

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Simple, unified interface to multiple Generative AI providers

Library and tool for annotating MAF files using Genome Nexus Webserver API

A python package for chromVAR

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

A toolkit for integrating histology and spatial transcriptomics - NeurIPS 2024

A large (+2500) collection of color maps for Python

Contextual AI models for single-cell protein biology

A gene expression signature scoring Python package.

A Python package to make publication-ready but customizable coefficient plots.

A comprehensive toolkit for mutational signature analysis

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

boilerplate for reproducible and transparent science

dalmatian is a collection of high-level companion functions for Firecloud and FISS.

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

Nimfa: Nonnegative matrix factorization in Python

In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarS…

R package to create cell pictures.

R package for Pathway RespOnsive GENe activity inference

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

Open source tools for computational pathology - Nature BME

Libraries for applying sparsification recipes to neural networks with a few lines of code, enabling faster and smaller models

Deep Learning Library for Single Cell Analysis