JiahuaQu

14-3-3_from_ANIA

2020_Wilk_COVID

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

acdc

Bug fixed version of acdc

addinslist

📜 Discover and install useful RStudio addins

Aire_target

Analyze_CyTOF_Using_Seurat

Cytometry by time-of-flight(CyTOF) data is very useful in studying the presence/absence of antigens/surface markers at single cell level. There are multiple tools to analyze CyTOF data but here I am presenting a tutorial of how one can quickly use Seurat (R package for scRNA-Seq analysis) for analyzing CyTOF data and understand the cellular and phenotypic diversity

AR-genes-gnomAD

Variant carrier rate - Svetlana

MEF-CBL0137

To reproduce it

Pipeline-for-RNA-sequencing-data-analysis-by-combination-of-Nextflow-and-R

My own pipeline

scSTAR

The R package source code and a demo script of scKinetics

JiahuaQu/Pipeline-for-RNA-sequencing-data-analysis-by-combination-of-Nextflow-and-R

My own pipeline

JiahuaQu/Aire_target

JiahuaQu/banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

JiahuaQu/ceLLama

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

JiahuaQu/cellranger

10x Genomics Single Cell Analysis

JiahuaQu/conga

Clonotype Neighbor Graph Analysis

JiahuaQu/DIANE

Dashboard for the Inference and Analysis of Networks from Expression data - From Alexandre So

JiahuaQu/dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

JiahuaQu/feature_engine

Feature engineering package with sklearn like functionality

JiahuaQu/ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

JiahuaQu/kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

JiahuaQu/Logan

Logan Unitigs and Contigs

JiahuaQu/MACD

Multi-omics atlas for common diseases

JiahuaQu/MMoCHi

MultiModal Classifier Hierarchy (MMoCHi)

JiahuaQu/monogenic-immune-health

This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Rachel Sparks, Nicholas Rachmaninoff, William W. Lau, Dylan C. Hirsch, Neha Bansal, ..., John S. Tsang: A Unified Metric of Human Immune Health (Nature Medicine, 2024)

JiahuaQu/omicverse

A python framework library for multi omics included bulk and single cell analysis with Python.

JiahuaQu/pan-NK

These are scripts for pan-cacner NK cells analyses.

JiahuaQu/parse_biosiences

scRNA-seq data after cytokine treatment, Parse_10M_PBMC_cytokines.h5ad

JiahuaQu/Practice-Building-R-Package

Practice building my own R packages

JiahuaQu/sc-SHC

Significance analysis for clustering single-cell RNA-sequencing data

JiahuaQu/ScaleMethyl

JiahuaQu/scDisInFact

JiahuaQu/scGPT

JiahuaQu/scrna-parameter-estimation

Direct estimation of mean and covariance from single cell RNA seq experiments

JiahuaQu/singularity-rstudio

A Singularity image definition file built on top of the Ubuntu 20.04 docker image with R, RStudio Server, and additional linux dependencies for common R packages installed.

JiahuaQu/spatial-bonemarrow-atlas

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"

JiahuaQu/starCAT

Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

JiahuaQu/StJude_PacBio-WDL-tutorial

JiahuaQu/TCAT_analysis

Code repository for TCAT analyses

JiahuaQu/tcrdist3

flexible CDR based distance metrics