zhumengyan's repositories
HCC2023
code for HCC analysis
AITL2023
code for our publication
cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
scFEA
single cell Flux Estimation Analysis (scFEA)
scrat
Sing Cell R Analysis Toolkit
AnnotationDatabase
annotation database for human genetics, genomics and epigenomics
pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
gggenes
➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
nanopore_related
nanopore sequencing
SingleR
SingleR: Single-cell RNA-seq cell types Recognition
Hannigan_CRCVirome_mBio_2018
Investigating the gut virus communities associated with colon cancer.
msigdf
Molecular Signatures Database (MSigDB) in a data frame
Bioinformatics-Resources
A curated list of resources for learning bioinformatics.
ImmuneResistance
This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".
HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
scRNA.seq.course
Analysis of single cell RNA-seq data course
interesting_papers
interesting papers
myblog
my blog using rblogdown
CNV-pepline
list softwares and papers about copy number variation
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
bioinfo_tasks
储存一些平时写的小脚本及帮助文件
TCAG-WGS-CNV-workflow
Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
DataWarehouse
DataSource
R_plot
ggplot2图形绘制学习模仿