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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

cajal3d-i2g

CAJAL3D Images to Graphs Pipeline

canu

A single molecule sequence assembler for genomes large and small.

coca

This repository is for the Caffe-based Object Classification and Annotation project, which uses convolutional neural networks to find biological structures in image data.

cupy

NumPy-like API accelerated with CUDA

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.

gffutils

GFF and GTF file manipulation and interconversion

h5py

HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

hed

code for Holistically-Nested Edge Detection

image-analogies

Generate image analogies using neural matching and blending.

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++

metacycle

An integrated R package to evaluate periodicity in large scale data

morphsnakes

Morphological snakes for image segmentation and tracking

mpipool

A Python MPI Pool

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

pims_nd2

Read nd2 files with the ND2SDK via ctypes

py-seg-tools

pygreentea

python-bittrex

Python library for the Bittrex API