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csci5481-2015

cuda

GPU-accelerated LIBSVM is a modification of the original LIBSVM that exploits the CUDA framework to significantly reduce processing time while producing identical results. The functionality and interface of LIBSVM remains the same. The modifications were done in the kernel computation, that is now performed using the GPU.

cudagsea

CUDA-accelerated Gene Set Enrichment Analysis

cudatree

Building random forests on GPU

cufflinks

curatedmetagenomicdata

Curated and processed metagenomic data through ExperimentHub

cxx-toolkit

cytofcore

R package for working with CyToF data

cytoscape

Cytoscape: an open source platform for network analysis and visualization

cytoscape.js

Graph theory (a.k.a. network) library for analysis and visualisation (compatible with CommonJS/Node.js/Browserify/Webpack, AMD/Require.js, npm, Bower, jspm, Meteor/Atmosphere, jQuery, and plain JS/JavaScript)

cytospade

Cytoscape plugin for SPADE

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

damethods2016

Code and manuscript files for Aaron and Arianne's differential abundance methodology manuscript.

dap

software package for integrative genetic association analysis

data-processor

Script to convert from VCF files to MAF files ready to be imported into cBioPortal

data-science-teaching

Teaching data science

dataflow-java

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

datalab-examples

Example Cloud Datalab iPython Notebooks for genomics use cases.

datasciencecoursera

datasciencespecialization.github.io

http://DataScienceSpecialization.github.io

datasharing

The Leek group guide to data sharing

dd3003

Parallel Computing: Theory - Hardware - Software with Special Focus on Multi-Core Programming

decomp

Infer large causal gene regulatory network from time series data by decomposing into smaller subnetworks.

deep-learning-columbia

deep-learning-ml-and-tensorflow

Examples of linear regression, logistic regression, and deep learning implementations using tensorflow. The iris data set is used to show how to load data from a csv to the tensorflow placeholders.

deep_learning_papers

A place to collect papers that are related to deep learning and computational biology

deeplearning

Deep Learning (Python, C, C++, Java, Scala, Go)

deeplearningtutorials

Deep Learning Tutorial notes and code. See the wiki for more info.

deeprtools

R tools for the German epigenome program DEEP (DEutsches Epigenom Programm)

degeprime

A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies