YaoXinZhi

spectra

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

MultiViewNMF

Partial Multi View Clustering via NMF

RWM

Local Community Detection in Multiple Netwrks

MultilayerExtraction

An R package to identify strongly connected vertex-layer communities in multilayer networks.

Gemini

SCAVENGE

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

NTS-NOTEARS

Code for paper: NTS-NOTEARS: Learning Nonparametric DBNs With Prior Knowledge

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

NetworkInference.jl

Methods for inferring undirected networks from data

CINEMA-OT

GSDensity_manuscript_code

DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

SoptSC

SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

liger

R package for integrating and analyzing multiple single-cell datasets

scMTNI

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

GCNG

using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions

network_inference_tutorials

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.

resVAE

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

QuickRecorder

A lightweight screen recorder based on ScreenCapture Kit for macOS / 基于 ScreenCapture Kit 的轻量化多功能 macOS 录屏工具

AgriGPTs

Research and Development of Agricultural Large Models|农业大模型研究与开发

awesome-graph-explainability-papers

Papers about explainability of GNNs

Kleborate

BLAH8-LLM-for-Rice-GARE

Bioregulatory Event Extraction using Large Language Models: A Case Study of Rice Literature

ChatGenTitle

🌟 ChatGenTitle：使用百万arXiv论文信息在LLaMA模型上进行微调的论文题目生成模型

genewalk

GeneWalk identifies relevant gene functions for a biological context using network representation learning

NLP4SciencePapers

Must-read papers on NLP for science.

Cancer-Alterome

Cancer-Alterome is a comprehensive and curated dataset that focuses on the investigation of regulatory events caused by gene alteration in the context of cancer.