Pinned Repositories
Arboretum2.0
The Arboretum 2.0 is the next release of the original code of Arboretum. It makes running Arboretum easier by taking care of initial cluster assignments.
drmn
DRMN with multi-task learning regression
grinch
GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
HiC-Reg
HiC-Reg is a tool to predict Hi-C contact counts from one-dimensional regulatory signals
merlin-p
A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)
MERLIN-P-TFA
Inferred networks and expression datasets for MERLIN-P+TFA project
mrtle
Multi-species regulatory network learning (Koch et al, Cell Systems 2017)
Roadmap_RegulatoryVariation
scMTNI
scRNAseq_NetInference
Roy lab's Repositories
Roy-lab/scMTNI
Roy-lab/grinch
GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
Roy-lab/drmn
DRMN with multi-task learning regression
Roy-lab/Roadmap_RegulatoryVariation
Roy-lab/scRNAseq_NetInference
Roy-lab/tgif
Tree-Guided Integrated Factorization (TGIF)
Roy-lab/Arboretum2.0
The Arboretum 2.0 is the next release of the original code of Arboretum. It makes running Arboretum easier by taking care of initial cluster assignments.
Roy-lab/Escarole
Expression State Clustering on Lineages (Escarole)
Roy-lab/merlin-p_inferred_networks
Roy-lab/Muscari
MUSCARI (Multi-task Spectral Clustering AlgoRIthm)
Roy-lab/new-member
References and resources for new members
Roy-lab/clade-specific_gene_sets
Scripts for selecting clade-specific gene sets from Arboretum result matrix
Roy-lab/compnetbiocourse
This repository has homework and assignment related files for the Computational Network Biology course BMI/CS 775.
Roy-lab/graph-representation-learning
Comparison of various node embedding algorithms on node classification downstream task
Roy-lab/graph_louvain_clustering
Roy-lab/MERLIN-VIZ
A visualization toolset for MERLIN Networks. Allows for direct user interaction.
Roy-lab/pancreatic_cell_grns
Repository for analysis done for XBP1 paper
Roy-lab/sc_ConsensusClustering
Scripts for unbiased clustering and consensus clustering
Roy-lab/subcluster_analysis
A repository of results from the Arboretum analysis to identify complex gene expression patterns in subpopulation subclusters.
Roy-lab/Tutorial_for_Aboretum-based_DE_geneset_analysis
A tutorial which includes Arboretum & findTransitionGenesets with an example dataset.
Roy-lab/afum_prior_net_constr
Files used for the prior network construction of Aspergillus fumigatus
Roy-lab/drmn_utils
Ancillary utilities for DRMN. Input processing and interpreting results.
Roy-lab/maize_autophagy
Roy-lab/merlin-auxillary
Downstream analysis for MERLIN inferred networks
Roy-lab/merlin-p_self_checkpoint
MERLIN-P with self checkpointing for Condor
Roy-lab/merlin-preprocess
Preprocessing methods for MERLIN.
Roy-lab/mvnmf
Roy-lab/roy-lab.github.io
Roy-lab/SCOTCH
A pytorch enabled implementation of the regularized non-negative matrix tri-factorization algorithm. This is Nvidia GPU compatible.
Roy-lab/utils
Roy lab in-house utilities