Suoqin Jin's Projects
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
R package of colors for the Buenrostro Lab
R vignettes for processing BUS format single-cell RNA-seq files
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
Standalone shiny server container for viewing CellChat object
Circular visualization in R
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
codes for the pseudotime analysis in our paper published in Cell Reports 2020
Make Complex Heatmaps
A SingleCell RNASeq pre-processing snakemake workflow
create alluvial plots with a single line of code
Single precision (float) matrices for R.
Google Drive Download Python Script
Fast, sensitive and accurate integration of single-cell data with Harmony
Notebooks and code for the book "Introduction to Machine Learning with Python"
Implementation of the Leiden algorithm called by reticulate in R.
A lite version of netSmooth for Single Cell RNA-seq data imputation
R pacakge for RNA velocity estimation with nonlinear models
NMF: A Flexible R package for Nonnegative Matrix Factorization (version 0.22.0)
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
An introduction to data science using Python and Pandas with Jupyter notebooks
Python Data Science Handbook: full text in Jupyter Notebooks
R Package for Producing and Visualizing Hillshaded Maps from Elevation Matrices, in 2D and 3D
An unsupervised approach for the integrative analysis of single-cell multi-omics data
A package to help convert different single-cell data formats to each other
An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data
Codes for computational analysis of scRNA-seq data of mouse motor neurons
R toolkit for single cell genomics