John Reid

DeLorean. R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.

pyseqan. Python interface to some of the SeqAn sequence analysis library functionality

pybool. A python package to infer Boolean regulatory networks

HAIS. Hamiltonian Annealed Importance Sampling (HAIS) in tensorflow

infpy. A python package that implements some models and inference techniques

JohnReid.github.io. John Reid's academic website

HMM. An implementation of various order discrete Markov models for sequence analysis. Coded in a generic programming style using C++ templates with a python interface.

bioinf-utilities. A collection of (largely python based) bioinformatic utilities

dotfiles. My configuration files (.tmux.conf, .vimrc, .bashrc, .gitconfig, etc)

STEME. An efficient accurate motif finder based on MEME and implemented using suffix arrays

Patilon. Python library to download flash files

PythonPackageTemplate. Template boilerplate code for how I like to set my python packages up

Cam-Bio-Big-Data. A directory of training available in Cambridge and around for basic bioinformatics processing and computational expertise in handling big data

myrrh. A library of useful C++ code, some related to boost.python, some related to the Seqan library

Cookbook. A collection of useful python code

boost-indexing-suite. Boost indexing suite v2 code developed by Raoul Gough.