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

Companion repository for our study on loss of Y chromosome (LOY) in lung cancer

Cell-type Specific Gene Networks and Drivers in Rheumatoid Arthritis

Interactome based Individual Specific Networks

Cell cluster Analysis with Variational Autoencoder using Conditional Hierarchy Of latent representioN

Single sample network reconstruction in R

Generate Robust Disease-Specific Response Signatures from the LINCS-L1000 Data

Smooth-quantile Normalization Adaptation for Inference of co-expression Links

Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks

An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo

🦠📇 Microbial genomes-to-report pipeline

PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

Node2vec2rank is an algorithm that can compare graphs to find their differences, e.g., in a case-control study that utilises gene regulatory networks.

Transcriptional Inference using Gene Expression and Regulatory data

Workflow to download and prepare TCGA data

DASH (Domain Aware Sparsity Heuristic) is a neural network pruning strategy that leverages domain-knowledge to obtain *meaningfully sparse* models.

pyEnGNet: optimized reconstruction of gene co-expression networks using multi-GPU

Source code for the paper "Fast and Accurate Inference of Gene Regulatory Networks through Robust Precision Matrix Estimation", by Passemiers et al.

netZooR is a network biology package implemented in R.

PHOENIX: a tool to infer biologically informed NeuralODEs describing genome-wide regulatory dynamics

A list of manuscripts/tools using diffusion on biological enttieis

Experiments for the paper "Higher-order correction of persistent batch effects in correlation networks".

COIN-OR Interior Point Optimizer IPOPT

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