Pinned Repositories
cobra-experiments
Experiments for the paper "Higher-order correction of persistent batch effects in correlation networks".
FENRIR
RNA-seq pipeline to detect viral reads
grand
GRAND database of gene regulatory networks.
matlab-panda
MATLAB implementation of PANDA & LIONESS algorithms
NetworkDataCompanion
An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo
neural_ODE
project: replacing the use of RNNs in gene-regulatory network prediction, with ODEs.
pandaR
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/pandaR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=pandaR.
phoenix
PHOENIX: a tool to infer biologically informed NeuralODEs describing genome-wide regulatory dynamics
pypanda
Python implementation of PANDA and LIONESS
yarn
YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
QuackenbushLab's Repositories
QuackenbushLab/phoenix
PHOENIX: a tool to infer biologically informed NeuralODEs describing genome-wide regulatory dynamics
QuackenbushLab/yarn
YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
QuackenbushLab/FENRIR
RNA-seq pipeline to detect viral reads
QuackenbushLab/pypanda
Python implementation of PANDA and LIONESS
QuackenbushLab/grand
GRAND database of gene regulatory networks.
QuackenbushLab/cobra-experiments
Experiments for the paper "Higher-order correction of persistent batch effects in correlation networks".
QuackenbushLab/matlab-panda
MATLAB implementation of PANDA & LIONESS algorithms
QuackenbushLab/NetworkDataCompanion
An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo
QuackenbushLab/pandaR
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/pandaR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=pandaR.
QuackenbushLab/neural_ODE
project: replacing the use of RNNs in gene-regulatory network prediction, with ODEs.
QuackenbushLab/MONSTER
QuackenbushLab/normFigures
Scripts to preprocess entire GTEx dataset and produce all rough figures
QuackenbushLab/tcga-data-nf
Workflow to download and prepare TCGA data
QuackenbushLab/DASH
DASH (Domain Aware Sparsity Heuristic) is a neural network pruning strategy that leverages domain-knowledge to obtain *meaningfully sparse* models.
QuackenbushLab/LOY_lung_cancer
Companion repository for our study on loss of Y chromosome (LOY) in lung cancer
QuackenbushLab/devbrim
Modify bipartite modularity maximization algorithm
QuackenbushLab/gpuzoo
Benchmarks of the gpuZoo implementations.
QuackenbushLab/QuackenbushLab.github.io
Landing page of the network science lab at Harvard Biostats
QuackenbushLab/tcga-data-supplement
supplementary notebooks and configuration files for the tcga-data-manuscript