Pinned Repositories
BenjaminDoran.github.io
bio-unidip-examples
Suplementary materials to "Unimodality Based Clustering Applied to Biological Motif Discovery"
Bio3DView.jl
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
LogoPlots.jl
Very basic plotting recipe for biological sequence motifs
motif-paper
Details application of UniDip to the problem of biologic motif discovery. We find that UniDip is able to preprocess DNA sequences such that MEME is able to find motifs 70% faster.
NeighborJoining.jl
Julia package for the neighbor joining algorithm
neo4j-graphaware-container
Docker compose and configuration files for running a Neo4j 3.3.1 container with GraphAware NLP and APOC plugins installed.
unidip
Python port of the Unidip clustering algorithm from: http://www.kdd.org/kdd2016/subtopic/view/skinny-dip-clustering-in-a-sea-of-noise
Urban-Sound-Classification
Urban Sound Classification: With Random Forest, SVM, DNN, RNN, and CNN Classifiers
BenjaminDoran's Repositories
BenjaminDoran/Urban-Sound-Classification
Urban Sound Classification: With Random Forest, SVM, DNN, RNN, and CNN Classifiers
BenjaminDoran/unidip
Python port of the Unidip clustering algorithm from: http://www.kdd.org/kdd2016/subtopic/view/skinny-dip-clustering-in-a-sea-of-noise
BenjaminDoran/bio-unidip-examples
Suplementary materials to "Unimodality Based Clustering Applied to Biological Motif Discovery"
BenjaminDoran/LogoPlots.jl
Very basic plotting recipe for biological sequence motifs
BenjaminDoran/NeighborJoining.jl
Julia package for the neighbor joining algorithm
BenjaminDoran/neo4j-graphaware-container
Docker compose and configuration files for running a Neo4j 3.3.1 container with GraphAware NLP and APOC plugins installed.
BenjaminDoran/BenjaminDoran.github.io
BenjaminDoran/Bio3DView.jl
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
BenjaminDoran/centos-spark
Builds Centos7 docker container image with Spark2.2 installed including dependencies
BenjaminDoran/checks
BenjaminDoran/docker-gmx
Docker automated build for GROMACS molecular dynamics program
BenjaminDoran/motif-paper
Details application of UniDip to the problem of biologic motif discovery. We find that UniDip is able to preprocess DNA sequences such that MEME is able to find motifs 70% faster.
BenjaminDoran/doran_resume
My CV
BenjaminDoran/epistlesofadifferenttime
BenjaminDoran/Filter10XData
WDL workflow to filter 10x data by sample
BenjaminDoran/GLMNet.jl
Julia wrapper for fitting Lasso/ElasticNet GLM models using glmnet
BenjaminDoran/help50
This is help50, a command-line tool that helps students understand error messages.
BenjaminDoran/help50-server
BenjaminDoran/Loom.jl
BenjaminDoran/Makie.jl
Interactive data visualizations and plotting in Julia
BenjaminDoran/Motif-Dataset
Bridge between JASPER and NCBI databases
BenjaminDoran/MultivariateStats.jl
A Julia package for multivariate statistics and data analysis (e.g. dimension reduction)
BenjaminDoran/NewickTree.jl
Newick formatted (phylogenetic) trees
BenjaminDoran/Phylo.jl
Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl
BenjaminDoran/ProgressMeter.jl
Progress meter for long-running computations
BenjaminDoran/section-checks
BenjaminDoran/seurat
R toolkit for single cell genomics
BenjaminDoran/seurat-docker
Docker container based of rocker/verse container with seurat and dependencies installed
BenjaminDoran/SpectralInference.jl
Spectral [phenotype/phylogenetic] Inference package
BenjaminDoran/Yggdrasil
Collection of builder repositories for BinaryBuilder.jl