supporting code for the multinomial single cell RNA-Seq paper

Multimodal Agentic EHR Co-Pilot Stops The Expensive Crisis Hiding in Electronic Health Records

Effective RNA Velocity Analysis: Mathematics, Implementation, and Application

A statistical model to analyze Tn-seq data

MSigDB gene sets for multiple organisms in a tidy data format. Jliu678 modified the way it treats mouse orthologs

Interactive single cell gene expression visualizations from Seurat contributed by jliu678

A toolkit of spatial transcriptomic analysis. The branches here contain Jliu678's pull requests that have been used to fix bugs but not merged.

Well-based scRNAseq has many more details than 10x scRNAseq to pay attention to in order to quantify features using Starsolo. Here, we discuss and present the snakemake pipline to quantify hERV, tr…

ERV gtf annotation is needed to quantify ERV from sequencing data. But the ERV gtf compatible with the latest mouse genome GRCm39 is not publicly available. Here I generated and validated the ERV g…

A snakemake pipline to quantify hERV, transgenes and genome from 10x single-cell RNAseq data

Modeling the deposition of infectious agents suggests that aerosolized drugs offer enhanced specificity

An R-based pipeline to analyse RNA-seq data. This pipeline performs quality control of reads, generates gene and transcript level counts, performs differential analysis, and gene pathway enrichment…

Quantify hERV and transgenes from Bulk-RNAseq using (bayesian) EM algorithm

The code that supports the findings in the PRCC paper published in Nature Communications

An R-based pipeline to analyse RNA-seq data. This pipeline performs quality control of reads, generates gene and transcript level counts, performs differential analysis, and gene pathway enrichment…

An R package allowing flexible base trimming and complete Fastq analysis on Windows System as fast and memory-efficient as linux