Steven Brown's repositories
bio-segmentation
This repository hosts simple examples of using deep networks to segment electron microscropy and other biological image data.
biom-format
The Biological Observation Matrix (BIOM) Format Project
bsnes
bsnes is a Super Nintendo (SNES) emulator focused on performance, features, and ease of use.
caffe
Caffe: a fast open framework for deep learning.
caffe_neural_models
Caffe model zoo and scripts
caffe_neural_tool
A C++ interface for the caffe library
canu
A single molecule sequence assembler for genomes large and small.
diamond
Accelerated BLAST compatible local sequence aligner.
empirical-JTK_CYCLE-with-asymmetry
This repository contains the code described in Hutchison, Maienschein-Cline, and Chiang et al. (2015) Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLoS Comput Biol 11(3): e1004094. doi:10.1371/journal.pcbi.1004094
ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
hed
code for Holistically-Nested Edge Detection
keras
Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.
lycon
A minimal and fast image library for Python and C++
openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
pandaseq
PAired-eND Assembler for DNA sequences
pbh5tools
A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5)
picrust
Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests
python-bittrex
Python library for the Bittrex API
python-snippets
Useful python code snippets.
q2-feature-table
QIIME 2 plugin supporting operations on feature tables.
qiime
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
scikit-learn
scikit-learn: machine learning in Python
sortmerna
SortMeRNA: a sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
ultrasound-nerve-segmentation
Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras
vispy
Main repository for Vispy