single-cell-genomics
There are 92 repositories under single-cell-genomics topic.
satijalab/seurat
R toolkit for single cell genomics
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
scverse/squidpy
Spatial Single Cell Analysis in Python
theislab/scarches
Reference mapping for single-cell genomics
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
theislab/cellrank
CellRank: dynamics from multi-view single-cell data
satijalab/seurat-wrappers
Community-provided extensions to Seurat
theislab/scgen
Single cell perturbation prediction
dpeerlab/Palantir
Single cell trajectory detection
kaizhang/SnapATAC2
Single-cell epigenomics analysis tools
samuel-marsh/scCustomize
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
mojaveazure/seurat-disk
Interfaces for HDF5-based Single Cell File Formats
enblacar/SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
satijalab/seurat-data
Dataset distribution for Seurat
yanwu2014/swne
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
satijalab/azimuth
A Shiny web app for mapping datasets using Seurat v4
parashardhapola/scarf
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
10XGenomics/loupeR
Convert Seurat objects to 10x Genomics Loupe files.
theislab/cpa
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
calico/scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
jsxlei/SCALEX
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
broadinstitute/single_cell_portal_core
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
mojaveazure/loomR
An R-based interface for loom files
GuangyuWangLab2021/cellDancer
Predict RNA velocity through deep learning
broadinstitute/single_cell_portal
Tutorials, workflows, and convenience scripts for Single Cell Portal
LiQian-XC/sctour
A deep learning architecture for robust inference and accurate prediction of cellular dynamics
robertaboukhalil/ginkgo
Cloud-based single-cell copy-number variation analysis tool
pinellolab/pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
quon-titative-biology/scAlign
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
nasqar/seuratv3wizard
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
WeiqiangZhou/BIRD
Big data Regression for predicting DNase I hypersensitivity
vertesy/Seurat.utils
Various utility functions for Seurat single-cell analysis
r3fang/snATAC
<<------ Use SnapATAC!!
immunogenomics/amp_phase1_ra
:ear_of_rice: Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.
microsoft/Nclusion.jl
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Qile0317/APackOfTheClones
Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.