An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

marker-based purification of cell types from single-cell RNA-seq datasets

Disk-based sparse matrix stats

Latent Embedding Multivariate Regression

Analysis related code deposit for manuscript.

A protocol for designing oligos for microbiome samples

A list of scRNA-seq analysis tools

Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

Code for the identification step for CSI-Microbes

supplementary tables and files

TACCO: Transfer of Annotations to Cells and their COmbinations

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data

Create anatograms using ggplot2

A repository for large-scale microbiome datasets, formatted for phyloseq

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

Assessing the quality of metagenome-derived genome bins using machine learning

The package wrapping the book, for deployment via the Bioconductor build system.

Repository for the building, sharing and editing of scRNAseq pipelines for the Lung Cell Atlas

This repository contains all code used for the Human Lung Cell Atlas project.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Automated Analysis of Multiplex Digital PCR Data