sqjin

CellChat

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

scAI

An unsupervised approach for the integrative analysis of single-cell multi-omics data

scEpath

An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data

CellChatShiny

Standalone shiny server container for viewing CellChat object

nlvelo

R pacakge for RNA velocity estimation with nonlinear models

easyalluvial

create alluvial plots with a single line of code

scRNA-seq-motor-neuron

Codes for computational analysis of scRNA-seq data of mouse motor neurons

awesome-single-cell

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

bigSCale2

Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data

ComplexHeatmap

Make Complex Heatmaps

gdrivedl

Google Drive Download Python Script

metadata_agedWound_CellReports2022

netSmooth

A lite version of netSmooth for Single Cell RNA-seq data imputation

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

signac

R toolkit for the analysis of single-cell chromatin data

BuenColors

R package of colors for the Buenrostro Lab

BUS_notebooks_R

R vignettes for processing BUS format single-cell RNA-seq files

circlize

Circular visualization in R

codes_CellReports2019

codes for the pseudotime analysis in our paper published in Cell Reports 2020

dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

float

Single precision (float) matrices for R.

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

introduction_to_ml_with_python

Notebooks and code for the book "Introduction to Machine Learning with Python"

NMF

NMF: A Flexible R package for Nonnegative Matrix Factorization (version 0.22.0)

PythonDataScienceHandbook

Python Data Science Handbook: full text in Jupyter Notebooks

sceasy

A package to help convert different single-cell data formats to each other

seurat

R toolkit for single cell genomics

seurat-object

Seurat-to-RNA-Velocity

A guide to using a Seurat object in conjunction with RNA Velocity

vioplot

Development version of vioplot R package (CRAN maintainer)