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

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

A list of scRNA-seq analysis tools

Survival Analysis and Visualization

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

Create anatograms using ggplot2

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

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

Latent Embedding Multivariate Regression

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

TACCO: Transfer of Annotations to Cells and their COmbinations

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

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

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

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

Code for the identification step for CSI-Microbes

Analysis of RNAseq data from (host-associated) microbial mixtures

supplementary tables and files

Disk-based sparse matrix stats

Course website for MCB 536 Tools for Computational Biology

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