Jianjiao Chen's repositories
algo
数据结构和算法必知必会的50个代码实现
anndata
Annotated data.
awesome-multi-omics
List of software packages for multi-omics analysis
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
citeseq_autoencoder
Integrative analysis of single-cell multi-omics data using deep learning
combes-organoid-paper
Analysis code and output for the Combes kidney organoid scRNA-seq paper
developer-roadmap
Roadmap to becoming a web developer in 2019
dynamo-notebooks
Tutorials of Dynamo usage cases and code to reproduce the manuscript
dynamo-release
Inclusive model of expression dynamics with scSLAM-seq and multiomics, vector field reconstruction and potential landscape mapping
lczero-training
For code etc relating to the network training process.
netSmooth
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
PIVOT
Platform for Interactive analysis and Visualization Of Transcriptomics data
pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
SAVER
Single-cell RNA-seq Gene Expression Recovery
SCENIC
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
simple-bash-scripts
A collection of simple Bash scripts
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
variant
Wrap up your bash scripts into a modern CLI today. Graduate to a full-blown golang app tomorrow.