41 Open source projects that are alternatives of or similar to GNE

OpenANE: the first Open source framework specialized in Attributed Network Embedding. The related paper was accepted by Neurocomputing. https://doi.org/10.1016/j.neucom.2020.05.080

Fast visualization tool for large-scale and high dimensional single-cell data

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

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Inference of switch-like differential expression along single-cell trajectories

Make rapid visualizations of RNA-seq data in R

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Interactive R package to quantify, analyse and visualise alternative splicing

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

📊 Gene expression in neuroexpresso database

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

GREIN : GEO RNA-seq Experiments Interactive Navigator

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Transcripts annotation and GO enrichment Fisher tests

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Differential Gene Correlation Analysis

TCGA data acquisition and processing for Project Cognoma

Spatial alignment of single cell transcriptomic data.

R package to access DoRothEA's regulons

A distributed graph deep learning framework.

Must-read papers on network representation learning (NRL) / network embedding (NE)

A curated list of network embedding techniques.

An Open-Source Package for Network Embedding (NE)

A collection of important graph embedding, classification and representation learning papers with implementations.

A collection of real-world networks/graphs for Network Embedding

Network Representation Learning with Rich Text Information (IJCAI 2015)

Code for CIKM'18 paper, Linked Causal Variational Autoencoder for Inferring Paired Spillover Effects.

An implementation of "Fusing Structure and Content via Non-negative Matrix Factorization for Embedding Information Networks".

Easing Embedding Learning by Comprehensive Transcription of Heterogeneous Information Networks(KDD'18)

Source code for AAAI 2019 paper "Relation Structure-Aware Heterogeneous Information Network Embedding"

Friends Recommendation and Link Prediction in Social Netowork

Profiling and Deanonymizing Ethereum Users

The reference implementation of FEATHER from the CIKM '20 paper "Characteristic Functions on Graphs: Birds of a Feather, from Statistical Descriptors to Parametric Models".

Tri-Party Deep Network Representation, IJCAI-16

A list of data mining and machine learning papers that I implemented in 2019.

Representation learning-based graph alignment based on implicit matrix factorization and structural embeddings

Source code and datasets of IJCAI2017 paper "TransNet: Translation-Based Network Representation Learning for Social Relation Extraction".

MixGCF: An Improved Training Method for Graph Neural Network-based Recommender Systems, KDD2021