NailouZhang

2020_iPS_Lung_Differentiation

Reproducibility repo accompanying Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian J. Theis, Herbert B. Schiller and Micha Drukker "Single cell trajectory mapping of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors".

5years

altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

AnalysisScripts

A motley collection of scripts used for analysis of high-throughput sequencing data

Analyze-Unmapped-Reads

This script is used for the analysis of unmapped reads from next generation sequencing (NGS) data.

AnnotateVariants

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq

ARMT

arriba

Fast and accurate gene fusion detection from RNA-Seq data

AS_Analysis_myeloid_neoplasms

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

NailouZhang/Analyze-Unmapped-Reads

This script is used for the analysis of unmapped reads from next generation sequencing (NGS) data.

NailouZhang/AnnotateVariants

This is a pipeline for variant annotation in the diagnosis of rare genetic disorders. It relies on open source data and has instructions for software installs.

NailouZhang/arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq

NailouZhang/ARMT

NailouZhang/assemblage

A Bioinformatics toolkit to assemble and annotate bacterial genomes.

NailouZhang/AutoDock-GPU

AutoDock for GPUs and other accelerators

NailouZhang/bohra

A pipeline for bioinformatics analysis of bacterial genomes

NailouZhang/cellrank_notebooks

Tutorials and figures for CellRank

NailouZhang/covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

NailouZhang/docker-stacks

Ready-to-run Docker images containing Jupyter applications

NailouZhang/drugbank_downloader

Don't worry about DrugBank licensing - write code that knows how to download it automatically

NailouZhang/dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

NailouZhang/flair

Full-Length Alternative Isoform analysis of RNA

NailouZhang/free

翻墙、免费翻墙、免费科学上网、免费节点、免费梯子、免费ss/v2ray/trojan节点、蓝灯、谷歌商店、翻墙梯子

NailouZhang/igvShiny

an htmlwidget version of igv, for RStudio and Shiny apps

NailouZhang/isotools

NailouZhang/Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

NailouZhang/Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

NailouZhang/Notes

java/Linux/Windows/macOS notes

NailouZhang/ntLink

Assembly scaffolder using long reads and minimizers

NailouZhang/SARS2_RBD_Ab_escape_maps

Interactive visualization of deep mutational scanning maps of mutations to SARS-CoV-2 RBD that escape antibody or sera binding

NailouZhang/SARSr-CoV_homolog_survey

Survey of ACE2 binding specificities among SARS-related CoV homologs

NailouZhang/scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

NailouZhang/seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

NailouZhang/single-cell-papers-with-code

Papers with code for single cell related papers

NailouZhang/smrnaseq

A small-RNA sequencing analysis pipeline

NailouZhang/splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

NailouZhang/tigmint

⛓ Correct misassemblies using linked AND long reads

NailouZhang/time2splice

Method to identify temporal and sex-specific alternative splicing from multi-omic data, specifically RNA-seq + (CUT&RUN or ChIP-seq).

NailouZhang/Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level