JunjuanZheng

ASpli

BioC current release of ASpli

AS_Analysis_myeloid_neoplasms

This repository contains the scripts used for the 2020 paper "Complex landscapes of alternative splicing in myeloid neoplasms"

GeomBarSignif

An accessible R function for significance drawing.

IRseq

CovidEpiMap

Single cell epitope mapping in COVID-19.

r

my R codes depository

scRNAseq-Lung

Collaboration with Renat Shaykhiev (res2003@med.cornell.edu) for lung development project

CITE-seq-TCR_paper

inferCC

Lung cancer 10X analysis

yipCat

yipCat package to realize some functional tools

covid-placenta

Analysis of single cell RNA-seq data from the fetal-maternal interface of COVID-19 positive mothers

cml_007_manu

Code related to NordCML 007 immunological substudy manuscript

SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

fgsea

Fast Gene Set Enrichment Analysis

SEVA

Code for analyses in Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer

cellphonedb

CGATPipelines

Collection of CGAT NGS Pipelines

NGS-Analysis-Notes

Notes for Routine NGS Analysis

asap

Parallelized alternative splicing analysis using MISO, rMATS and Whippet

process_rMATS_output

processing rMATS(4.0.2) output files and get AS events in single sample

cookiecutter-de_analysis_skeleton

Skeleton for new differential expression analysis project.

booknote

visit my gitbook

siri

intron-retention-paper

intron_retention_analysis_senescence

Intron retention analysis for RNA-seq of cellular senescence models

om-nf-rnaseq

omplotr

store plot functions & themes for onmath projects

ocular_transcriptomes_pipeline

A Snakemake pipeline for constructing de novo*transcriptomes from the EiaD dataset

dox

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines