Pinned Repositories
ChromBERT
ChromBERT: A pre-trained foundation model for context-specific transcription regulatory network
CondSig
A computational framework to detect Condensate-like chromatin-associated proteins co-occupancy Signatures
CStreet
CStreet is a cell state trajectory inference method for time-series single-cell RNA-seq data. It is written in Python (3.6, 3.7 or 3.8) and is available as a command line tool and a Python library to meet the needs of different users.
FitCR
codes and supplemental tables for "Antibody-freely profiling transcription factor occupancy during early embryogenesis by FitCUT&RUN"
ImSpiRE
ImSpiRE is an Image features-aided Spatial Resolution Enhancement method for in situ capturing (ISC) datasets. It is written in Python 3.8 and requires CellProfiler 4.2.1. It is available as a command line tool, a Python library and a docker image to meet the needs of different users.
MethylTransition
A R package for the parameter estimation of DNA methylation transition in cell mitosis.
ncHMR_detector
Software package for non-classical HMR function
PCAR
PSPire
PSPire is a machine learning model based on integrated residue-level and structure-level features to predict phase-separating proteins. It is written in Python3 and is available as a command line tool.
wwang_bioinfo_tools
TongjiZhanglab's Repositories
TongjiZhanglab/ChromBERT
ChromBERT: A pre-trained foundation model for context-specific transcription regulatory network
TongjiZhanglab/PSPire
PSPire is a machine learning model based on integrated residue-level and structure-level features to predict phase-separating proteins. It is written in Python3 and is available as a command line tool.
TongjiZhanglab/PCAR
TongjiZhanglab/CondSig
A computational framework to detect Condensate-like chromatin-associated proteins co-occupancy Signatures
TongjiZhanglab/ImSpiRE
ImSpiRE is an Image features-aided Spatial Resolution Enhancement method for in situ capturing (ISC) datasets. It is written in Python 3.8 and requires CellProfiler 4.2.1. It is available as a command line tool, a Python library and a docker image to meet the needs of different users.
TongjiZhanglab/CStreet
CStreet is a cell state trajectory inference method for time-series single-cell RNA-seq data. It is written in Python (3.6, 3.7 or 3.8) and is available as a command line tool and a Python library to meet the needs of different users.
TongjiZhanglab/ncHMR_detector
Software package for non-classical HMR function
TongjiZhanglab/FitCR
codes and supplemental tables for "Antibody-freely profiling transcription factor occupancy during early embryogenesis by FitCUT&RUN"
TongjiZhanglab/MethylTransition
A R package for the parameter estimation of DNA methylation transition in cell mitosis.
TongjiZhanglab/MethylTransition_DataAnalysis
This repository contains the custom scripts of MethylTransition project.
TongjiZhanglab/wwang_bioinfo_tools
TongjiZhanglab/ADNP_Modulates_SINE_B2_CTCF
TongjiZhanglab/CAM
TongjiZhanglab/CHMs_during_mouse_development
TongjiZhanglab/CSPred
TongjiZhanglab/CTFPdetector
An R script for cell fate transcription factor pairs detection in lineage commitment process.
TongjiZhanglab/drseq
Dr.seq single cell RNA-seq QC and analysis pipeline
TongjiZhanglab/DrSeq2
TongjiZhanglab/MethylTransition_DataCollection
This repository contains the scripts to download the public datasets for MethylTransition project.
TongjiZhanglab/MHB
Source codes for MHB study
TongjiZhanglab/TSSCpath
TSSCpath constructs cell trajectory on time-series single-cell RNA-seq
TongjiZhanglab/zebrafish-maternal-loading