cplaisier

miRvestigator_www

A web server version of the miRvestigator framework.

offYerBack

Code to access cMonkey RData objects and provide the data in a Python friendly manner.

buildTFBSDB

Builds a Transcription Factor Binding Site (TFBS) database (DB) for use as an input to cMonkey via set enrichment.

offYerBackV2

A suite of tools to post process gene regulatory networks.

cmonkey-python

Python port of cMonkey, a machine-learning based method for clustering

FIRM

Framework for Inference of Regulation by miRNAs (FIRM)

BooleanDynamicModeling

Java library to simulate Boolean Dynamic models

booleannet

Boolean Network Modeling

CellFateReprogramming

Java project related to the paper "Cell fate reprogramming by control of intracellular network dynamics" (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004193)

cnvkit

Copy number variant detection from targeted DNA sequencing

diptest

Python/C implementation of Hartigan & Hartigan's dip test, based on Martin Maechler's R package

glioma_web

Website backing publication.

hopfieldNetworks

Hopfield Networks for visualizing the state space of different samples.

HopLand

inferCNV

Inferring CNV from Single-Cell RNA-Seq

isbIntoSysBio

R scripts for introduction to systems biology at ISB.

JohnsonCycleAlgorithm

Java library that implements the Jonhson Cycle algorithm and adapts it to the search for stable motifs.

libermate

LiberMate - A MATLAB to Python (SciPy/NumPy) Translator

Normalizer

Code for normalizing count data.

OncoMerge

Software to integrate somatic protein affecting mutations (PAMs) and copy number alterations (CNAs) for downstream computational analyses.

pyBinarize

Binarizes gene expression data using a k-means based approach that is ported from the R package Binarize.

pyega

EGA (European Genome-phenome archive) downloader

scater

Single cell analysis tools for expression from RNA-seq in R

smop

Small Matlab to Python compiler (Let APL be your guide and interpreter -- anonymous)

StableMotifs

Java library that implements the attractor finding method described in Chaos 23 (2) 025111, and the control method described in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1004193.

tcell_web

Mtb infection T cell regulatory network web site.

TF_network

TF_targets

Script to find TF regulators for a given input gene file.

Trans_eQTL_Hotspot_Viewer

Visualization of trans-eQTL hotspots for mouse genome.

viridis

Tools for quantitative analyses of diatom resilience.