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sclamons's Projects

bioscrape_distr icon bioscrape_distr

BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)

breeding_pool icon breeding_pool

Genetic Simulation, originally based of XKCD's what-if dnd character model of inheritance.

chibio icon chibio

ChiBio primary operating system.

gtfparse icon gtfparse

Parsing tools for GTF (gene transfer format) files

hamilton icon hamilton

A framework for quickly developing simulations of evolutionary experiments.

hypothesis icon hypothesis

Hypothesis is a powerful, flexible, and easy to use library for property-based testing. Forked for dev work

juliabox icon juliabox

Juliabox continues to run, but this codebase is no longer current.

keras icon keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

lw_quest_analysis icon lw_quest_analysis

An analysis of the D&D.Sci problem from LessWrong (https://www.lesswrong.com/posts/HsxT2cpPWYzTg9tpY/d-and-d-sci)

murraylab_tools icon murraylab_tools

Functions for building Echo picklists and directions for setting up source plates for the Echo. Mostly intended for setting up TX-TL experiments.

ped icon ped

MATLAB code for variable selection from microarray expression data by binomial regression with Penalized Euclidean Distance.

pyfastx icon pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

surface_crns icon surface_crns

Package for simulating and displaying chemical reaction networks (CRNs) on a surface.

tests-as-linear icon tests-as-linear

Common statistical tests are linear models (or: how to teach stats)

trimgalore icon trimgalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

xbase icon xbase

XBASE - a database and web framework for bacterial genomics and next-generation sequencing

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