A command-line tool to mitigate homology-based data leakage in sequence-to-expression models

Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.

Picarta AI Image Geolocalization API.

UCE is a zero-shot foundation model for single-cell gene expression data

Deep generative models for single-cell omics data

Decima is a Python library to train sequence models on single-cell RNA-seq data.

Invariant Representation learning

Quick pre-QC knee plots for barcode based scRNAseq data

Join subcellular Visium HD bins into cells

Pipeline for designing custom probes against human genes

A declarative interactive genomics visualization library for Python.

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

Gaussian process regression package for counts data with negative binomial and zero-inflated negative binomial likelihoods

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

Scentinel is a probabilistic ensemble framework designed for mapping large single-cell (sc) multi-omic datasets using either transductive or inductive transfer learning. The framework operates on p…

scVI extension for unspliced RNA

cell2module: decomposing scRNA and scATAC cell identity into gene modules using count-based Bayesian NMF

Scentinel is a probabilistic ensemble framework designed for mapping large single-cell (sc) multi-omic datasets using either transductive or inductive transfer learning. The framework operates on p…

A method for analyzing scATAC-seq experiments.

MLX: An array framework for Apple silicon

Defense Against the Dark Arts

sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale