Roy lab

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.
Language:C2 4 11
drmn
DRMN with multi-task learning regression
Language:C5 4 11
grinch
GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
Language:C9 6 31
HiC-Reg
HiC-Reg is a tool to predict Hi-C contact counts from one-dimensional regulatory signals
Language:C11 3 43
merlin-p
A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)
Language:C5 6 26
mrtle
Multi-species regulatory network learning (Koch et al, Cell Systems 2017)
Language:C2 4 02
Roadmap_RegulatoryVariation
Language:C4 4 00
scMTNI
Language:C30 5 226
scRNAseq_NetInference
Language:Jupyter Notebook4 4 53
tgif
Tree-Guided Integrated Factorization (TGIF)
Language:C3 4 10

Roy lab's Repositories

Roy-lab/scMTNI
Language:C30 5 226
Roy-lab/grinch
GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
Language:C9 6 31
Roy-lab/drmn
DRMN with multi-task learning regression
Language:C5 4 11
Roy-lab/Roadmap_RegulatoryVariation
Language:C4 4 00
Roy-lab/scRNAseq_NetInference
Language:Jupyter Notebook4 4 53
Roy-lab/tgif
Tree-Guided Integrated Factorization (TGIF)
Language:C3 4 10
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.
Language:C2 4 11
Roy-lab/MERLIN-P-TFA
Inferred networks and expression datasets for MERLIN-P+TFA project
Language:HTML2 4 00
Roy-lab/Escarole
Expression State Clustering on Lineages (Escarole)
Language:C1 4 21
Roy-lab/graph-representation-learning
Comparison of various node embedding algorithms on node classification downstream task
Language:Jupyter Notebook1 3 00
Roy-lab/merlin-p_inferred_networks
1 3 11
Roy-lab/Muscari
MUSCARI (Multi-task Spectral Clustering AlgoRIthm)
Language:C1 3 00
Roy-lab/new-member
References and resources for new members
1 6 00
Roy-lab/clade-specific_gene_sets
Scripts for selecting clade-specific gene sets from Arboretum result matrix
Language:C0 4 00
Roy-lab/compnetbiocourse
This repository has homework and assignment related files for the Computational Network Biology course BMI/CS 775.
Language:Jupyter Notebook0 4 00
Roy-lab/MERLIN-VIZ
A visualization toolset for MERLIN Networks. Allows for direct user interaction.
Language:JavaScript0 3 00
Roy-lab/pancreatic_cell_grns
Repository for analysis done for XBP1 paper
Language:Python0 5 00
Roy-lab/sc_ConsensusClustering
Scripts for unbiased clustering and consensus clustering
Language:MATLAB0 4 00
Roy-lab/subcluster_analysis
A repository of results from the Arboretum analysis to identify complex gene expression patterns in subpopulation subclusters.
Language:HTML0 3 00
Roy-lab/Tutorial_for_Aboretum-based_DE_geneset_analysis
A tutorial which includes Arboretum & findTransitionGenesets with an example dataset.
Language:C0 3 00
Roy-lab/afum_prior_net_constr
Files used for the prior network construction of Aspergillus fumigatus
Language:Python4 01
Roy-lab/maize_autophagy
Language:C4 0
Roy-lab/merlin-auxillary
Downstream analysis for MERLIN inferred networks
Language:C4 01
Roy-lab/merlin-p_self_checkpoint
MERLIN-P with self checkpointing for Condor
Language:C4 0
Roy-lab/merlin-preprocess
Preprocessing methods for MERLIN.
Language:HTML4 0
Roy-lab/mvnmf
Language:C5 0
Roy-lab/PoplarATACAnalysis
Analysis of ATAC-Seq data from the stem of the Poplar (Populus trichocarpa) plant derived from the singleron-RD CeleScope platform using ArchR
Language:Shell
Roy-lab/roy-lab.github.io
3 0
Roy-lab/SCOTCH
A pytorch enabled implementation of the regularized non-negative matrix tri-factorization algorithm. This is Nvidia GPU compatible.
Language:Python
Roy-lab/SCOTCH_CPP
Language:C++