Jiale Chen

I work on sequencing data — coverage statistics, single-cell pipelines, and the small command-line tools that sit between them.

What I work on Code Contact

Read depth across a region: coverage piles up over exons and drops to noise between them. Getting this number right is most of the job.

What I work on

Most of what I build sits between raw sequencer output and something a biologist can act on. That means depth and coverage statistics you can defend, single-cell pipelines that produce the same answer twice, and file handling fast enough that nobody thinks about it.

I keep the tools small and public. If a step in an analysis took me a week to get right, the script for it should take someone else an afternoon.

Code

scRNA-seq-analysis
A single-cell RNA-seq pipeline covering the problems you actually hit — QC thresholds, batch handling, annotation — rather than the happy path.
sequencing-read-depth-calculate
Calculates sequencing read depth from NGS data, so coverage claims in a methods section have something behind them.
fmd5sum
A faster md5sum for the multi-terabyte transfers that genomics runs on.

Install from PyPI
Deep-Learning-in-Genomics
Notes and experiments on applying deep learning to genomics problems.
CELR-D-22-00015
Analysis code for Li et al., Cell Regeneration, 2022.
DeepSeek-handbook
DeepSeek 使用手册 — a practical Chinese-language guide to working with the models.

All repositories on GitHub