sclamons's repositories
surface_crns
Package for simulating and displaying chemical reaction networks (CRNs) on a surface.
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.
bioscrape_distr
BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)
Breeding_Pool
Genetic Simulation, originally based of XKCD's what-if dnd character model of inheritance.
ChiBio
ChiBio primary operating system.
chitin-simulator
A GUI-based surface CRN simulator, written in Rust
coli_crew_project_3
CS155 Project 3, by the Coli Crew (John Marken & Samuel Clamons)
DNA_Instrument
An audio debugger for DNA
gtfparse
Parsing tools for GTF (gene transfer format) files
hamilton
A framework for quickly developing simulations of evolutionary experiments.
hypothesis
Hypothesis is a powerful, flexible, and easy to use library for property-based testing. Forked for dev work
JuliaBox
Juliabox continues to run, but this codebase is no longer current.
keras
Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.
LW_Quest_Analysis
An analysis of the D&D.Sci problem from LessWrong (https://www.lesswrong.com/posts/HsxT2cpPWYzTg9tpY/d-and-d-sci)
Porechop-1
adapter trimmer for Oxford Nanopore reads
pyfastx
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
tests-as-linear
Common statistical tests are linear models (or: how to teach stats)
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
xbase
XBASE - a database and web framework for bacterial genomics and next-generation sequencing