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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

buencolors

R package of colors for the Buenrostro Lab

bus_notebooks_r

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

cellchat

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

cellchatshiny

Standalone shiny server container for viewing CellChat object

circlize

Circular visualization in R

clustergrammer2

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

codes_cellreports2019

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

complexheatmap

Make Complex Heatmaps

dropseqpipe

A SingleCell RNASeq pre-processing snakemake workflow

easyalluvial

create alluvial plots with a single line of code

float

Single precision (float) matrices for R.

gdrivedl

Google Drive Download Python Script

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"

leiden

Implementation of the Leiden algorithm called by reticulate in R.

metadata_agedwound_cellreports2022

netsmooth

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

nlvelo

R pacakge for RNA velocity estimation with nonlinear models

nmf

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

pydata-book

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

python-for-data-analysis

An introduction to data science using Python and Pandas with Jupyter notebooks

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

rayshader

R Package for Producing and Visualizing Hillshaded Maps from Elevation Matrices, in 2D and 3D

scai

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

sceasy

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

scepath

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

scrna-seq-motor-neuron

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

seurat

R toolkit for single cell genomics