Xi Chen's repositories
scATAC_snakemake
Snakemake pipeline for plate scATAC-seq processing
SUSTech-BIO210
Course material for the undergraduate biostatistics course (BIO210) at SUSTech
SUSTech-BIOS201
Course content for BIOS201 at SUSTech
LLMs-from-scratch
Implementing a ChatGPT-like LLM from scratch, step by step
LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
awesome-long-reads
tools and notes for long reads analysis
BI-BE-CS-183-2023
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
Blacklist
Application for making ENCODE Blacklists
cellhint
A tool for semi-automatic cell type harmonization and integration
datavisguide
Introductory guide to the art and science of data visualisation. Insights, advice, and examples (with code) to make data outputs more readable, accessible, and impactful.
landchad
Landchad.net Website Tutorial Page
NSForest
A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
numpy-ml
Machine learning, in numpy
picasso
Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.
Python
All Algorithms implemented in Python
python-genomics
A set of files to do genomics analysis on python
RMEJLBASBMP_2024
Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"
seqspec
machine-readable file format for genomic library sequence and structure
singleCellHaystack-py
A Python implementation of singleCellHaystack
STACAS
Sub-Type Anchoring Correction for Alignment in Seurat
topometry
Systematically learn and evaluate manifolds from high-dimensional data