Zestel Shen's repositories
Reproductions-of-public-code
Testing and organization of public code
metaspine
Config files for my GitHub profile.
weekly
生信爱好者周刊（每周日发布）
cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Awesome-Reproducible-Analysis-of-Single-Cell-Papers
A curated list of awesome reproducible papers in single-cell omics
Awesome-Bio-Foundation-Models
A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.
ktplots
Some tools for plotting single-cell data
ecotyper
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
ProcessTrialtrove
Software for analyzing the data in the trialtrove database
infercna
Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
mamba
The Fast Cross-Platform Package Manager
ilus-WES-WGS-
A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
scFEA
single cell Flux Estimation Analysis (scFEA) Try the below web server!
Pipelines-Wrappers
Shell wrappers for common NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, WGS, etc.
scanorama
Panoramic stitching of single cell data
cutTag-pipeline
Pipeline for Cut&Tag analysis
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
atac-seq-pipeline
ENCODE ATAC-seq pipeline
single-cell-papers-with-code
Papers with code for single cell related papers
proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
PSlab
Bioinformatic analyses run in PS lab
bollito
A single-cell RNA-seq pipeline