Jian-Guo Zhou's Projects
Genomic Correlates of Response to Immune Checkpoint Inhibition in Small Cell Lung Cancer
Single-cell atlas of SCLC leveraging scRNA-seq, MIBI, and Vectra imaging, as part of the Human Tumor Atlas Network
Normalization for single cell RNA-seq data
Single Cell Rna-seq ANalysis
Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution
BC Cancer single-cell RNA-seq digestion method paper
Detect doublets in single-cell RNA-seq data
R package for modeling single cell UMI expression data using regularized negative binomial regression
In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
Toolkit for processing sequences in FASTA/Q formats
R toolkit for single cell genomics
Shain Lab UCSF Post Mutect2 Filters
An interactive web portal for exploring immuno-oncology data
🌲 An easy-to-use and scalable toolkit for genomic alteration (mutational) signature analysis and visualization in R
Simplify GO enrichment results
Pipeline for exploring metebolic heterogeneity at single-cell resolution
Here we provide the DATA ACCESS AGREEMENT for single T cell data which deposited in the European Genome-phenome Archive with the access number EGAS00001002791
Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
SingleCellNet: classify single cells across species and platforms
Gene set enrichment analysis for single-cell RNAseq data
Multi-platform, free open source software for visualization and image computing.
Extension for 3D Slicer that allows the application to be used from Jupyter notebook
:exclamation: This is a read-only mirror of the CRAN R package repository. smoothHR — Smooth Hazard Ratio Curves Taking a Reference Value
Single Nucleus Analysis Package for ATAC-seq
Clustering scRNAseq by genotypes
R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data