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_tool
A C++ interface for the caffe library
canu
A single molecule sequence assembler for genomes large and small.
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.
gffutils
GFF and GTF file manipulation and interconversion
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