LingyiC

d2l-zh

《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被70多个国家的500多所大学用于教学。

BioGPT

scRNA-seq_notes

A list of scRNA-seq analysis tools

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Awesome-Scientific-Language-Models

A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery

tcga_example

xCell

Cell types enrichment analysis

scRNA.seq.datasets

Collection of public scRNA-Seq datasets used by our group

annotables

R data package for annotating/converting Gene IDs

cceval

CrossCodeEval: A Diverse and Multilingual Benchmark for Cross-File Code Completion (NeurIPS 2023)

SingleCellWorkshop

scGAN

Realistic in silico generation and augmentation of single cell RNA-seq data using Generative Adversarial Neural Networks

CNNC

covolutional neural network based coexpression analysis

AutoClass

NetworkInference.jl

Methods for inferring undirected networks from data

SCODE

SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

DRComparison

Comparison of dimensionality reduction methods

scDesign2

An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated

SingleCellLineage

Updated scripts and pipelines for processing GESTALT data at single-cell resolution

STRIDE

STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using single-cell transcriptomics data.

SAFEclustering

SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data

inferCC

Lung cancer 10X analysis

Symphony

Symphony algorithm for inference of cell type specific gene regulatory networks from scRNA-seq and ATAC-seq

scifiRNA-seq_publication

The million-scale method for single-cell analysis

scMappR

the scMappR developmental package

CASCC

CASCC: A co-expression assisted single-cell RNA-seq data clustering method

2DImpute

Imputation in single cell RNA sequencing data using correlations from two dimensions

dli_gpr

GP regression model for DLI therapy data for CML

ORdensity