cplaisier Goto Github PK

booleandynamicmodeling

Java library to simulate Boolean Dynamic models

booleannet

Boolean Network Modeling

buildtfbsdb

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

cancer-mirna-regulatory-network

A database containing the predictions for the Cancer miRNA-Regulatory Network.

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)

cmonkey

cMonkey integrated biclustering algorithm

cmonkey-python

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

cnvkit

Copy number variant detection from targeted DNA sequencing

d3

A JavaScript visualization library for HTML and SVG.

diptest

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

firm

Framework for Inference of Regulation by miRNAs (FIRM)

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.

keggtap

An interface to get the latest KEGG data and compare it to sets of genes for over-representation.

libermate

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

mirvestigator

Identify miRNA that binds to a PSSM motif from 3' UTR.

mirvestigator_standalone

Stand alone version of miRvestigator HMM that takes as input a FASTA stlyed PSSM file.

mirvestigator_www

A web server version of the miRvestigator framework.

normalizer

Code for normalizing count data.

offyerback

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

offyerbackv2

A suite of tools to post process gene regulatory networks.

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

sequence-extractor

Extracts sequence for promoter and 3' UTR regions. Eventually will be developed to extract all potential cis-regulatory regions.