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awesome-deep-learning-single-cell-papers

awesome-foundation-model-single-cell-papers

awesome-single-cell

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

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

bpcells

Scaling Single Cell Analysis to Millions of Cells

celescope

Single Cell Analysis Pipelines

cell2location

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

cellbox

CellBox: Interpretable Machine Learning for Perturbation Biology

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellchat-old

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

cellranger

10x Genomics Single Cell Analysis

cellrank

CellRank: dynamics from multi-view single-cell data

celltalker

Inference of cell-cell communication from single-cell RNAseq data

cellxgene

An interactive explorer for single-cell transcriptomics data

clustering_on_transcript_compatibility_counts

Clustering cells from single cell RNA seq assays

conditional-ddpm

A simple PyTorch implementation of conditional denoising diffusion probabilistic models (DDPM) on MNIST, Fashion-MNIST, and Sprite datasets

course-project-bt5240

Course Project of BT5240 - Computational Systems Biology, IIT Madras; Deep generative approach to model single-cell expression data of human embryoid bodies

deep-generative-modeling-and-probabilistic-dimension-reduction

Re-implemntation of scVI (a deep generative model) using PyTorch, PyTorch Lightning, and Pyro

deepcdr

Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network

deepcell-tf

Deep Learning Library for Single Cell Analysis

deepspeed

DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

desc

Deep Embedding for Single-cell Clustering

dgm4sca

CS280 Project: Deep generative model for single-cell annotation

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

einops

Flexible and powerful tensor operations for readable and reliable code (for pytorch, jax, TF and others)

episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

evo

Biological foundation modeling from molecular to genome scale

gears

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

glue

Graph-linked unified embedding for single-cell multi-omics data integration

harmonizationscanvi

Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper