NailouZhang's repositories
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
assemblage
A Bioinformatics toolkit to assemble and annotate bacterial genomes.
AutoDock-GPU
AutoDock for GPUs and other accelerators
bohra
A pipeline for bioinformatics analysis of bacterial genomes
cellrank_notebooks
Tutorials and figures for CellRank
covariants
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
docker-stacks
Ready-to-run Docker images containing Jupyter applications
drugbank_downloader
Don't worry about DrugBank licensing - write code that knows how to download it automatically
dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
flair
Full-Length Alternative Isoform analysis of RNA
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
igvShiny
an htmlwidget version of igv, for RStudio and Shiny apps
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.
Long-Read-Proteogenomics
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
Notes
java/Linux/Windows/macOS notes
ntLink
Assembly scaffolder using long reads and minimizers
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
SARSr-CoV_homolog_survey
Survey of ACE2 binding specificities among SARS-related CoV homologs
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
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.
single-cell-papers-with-code
Papers with code for single cell related papers
smrnaseq
A small-RNA sequencing analysis pipeline
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
tigmint
⛓ Correct misassemblies using linked AND long reads
time2splice
Method to identify temporal and sex-specific alternative splicing from multi-omic data, specifically RNA-seq + (CUT&RUN or ChIP-seq).
Whippet.jl
Lightweight and Fast; RNA-seq quantification at the event-level