chentao's repositories
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
BITFAM
BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
caffe
Caffe: a fast open framework for deep learning.
cellrank_reproducibility
CellRank's reproducibility repository.
celltypist
A tool for semi-automatic cell type classification, harmonization and integration
deeplearning-notes
Notes for Deep Learning Specialization Courses led by Andrew Ng.
EPIMAP_ANALYSIS
Epimap processing and analysis code repository
examples
A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.
gget
🧬 gget enables efficient querying of genomic reference databases
lab-website-template
(Pre-release) An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more
Machine-Learning-is-ALL-You-Need
🔥🌟《Machine Learning 格物志》: ML + DL + RL basic codes and notes by sklearn, PyTorch, TensorFlow, Keras & the most important, from scratch!💪 This repository is ALL You Need!
math
🧮 Path to a free self-taught education in Mathematics!
MELD
Quantifying experimental perturbations at single cell resolution
Palantir
Single cell trajectory detection
PALMER
Pre-mAsking Long reads for Mobile Element inseRtion
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
PyTorch-GAN
PyTorch implementations of Generative Adversarial Networks.
Rstringtie
Transcriptome sequencing assembly
Scissor
Scissor package
SCP
Single Cell Pipeline
SingleCell
R package of integrated analysis of single cell data
Tangram
Spatial alignment of single cell transcriptomic data.
TCRGP
TCRGP, a novel Gaussian process method that can predict if TCRs recognize certain epitopes. This method can utilize different CDR sequences from both TCRα and TCRβ chains from single-cell data and learn which CDRs are important in recognizing the different epitopes.
tfmodisco
TF MOtif Discovery from Importance SCOres