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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

centos-spark

Builds Centos7 docker container image with Spark2.2 installed including dependencies

checks

docker-gmx

Docker automated build for GROMACS molecular dynamics program

doran_resume

My CV

epistlesofadifferenttime

filter10xdata

WDL workflow to filter 10x data by sample

glmnet.jl

Julia wrapper for fitting Lasso/ElasticNet GLM models using glmnet

help50

This is help50, a command-line tool that helps students understand error messages.

help50-server

logoplots.jl

Very basic plotting recipe for biological sequence motifs

loom.jl

motif-dataset

Bridge between JASPER and NCBI databases

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.

multivariatestats.jl

A Julia package for multivariate statistics and data analysis (e.g. dimension reduction)

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.

newicktree.jl

Newick formatted (phylogenetic) trees

phylo.jl

Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl

progressmeter.jl

Progress meter for long-running computations

section-checks

seurat

R toolkit for single cell genomics

seurat-docker

Docker container based of rocker/verse container with seurat and dependencies installed

skinny-dip

Code and supplementary material from the KDD 2016 paper "Skinny-dip: Clustering in a sea of noise" by Samuel Maurus and Claudia Plant.

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

yggdrasil

Collection of builder repositories for BinaryBuilder.jl