Computational Biology and Computational Learning @ UCI

Login: uci-cbcl

Company: null

Location: Irvine, CA, USA

email: uci-cbcl@googlegroups.com

Blog: http://cbcl.ics.uci.edu

Members

1. Daniel Newkirk
2. Jake Biesinger
3. Yifei Chen
4. Yi Li
5. Yuanfeng Wang
6. null

Repositories

AREM

AREM -- Aligning Reads by Expectation-Maximization

ChestXRay

null

consensus-search

Simple consensus search script as used in our *genesis* Xenopus paper

CoreNLP

Stanford CoreNLP: A Java suite of core NLP tools.

DanQ

A hybrid convolutional and recurrent neural network for predicting the function of DNA sequences

DeepCADD

null

DeepCons

Understanding sequence conservation with deep learning

DeepEM-for-Weakly-Supervised-Detection

MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection

DeepLung

WACV18 paper "DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification"

D-GEX

Deep learning for gene expression inference

EXTREME

An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data

FactorNet

A deep learning package for predicting TF binding

GBMCI

The implementation of gradient boosting machine for concordance index learning.

genomix

Parallel genome assembly using Hyracks

HLA-bind

Amino acid embedding and Convolutional Neural Network for HLA Class I-peptide binding prediction

HTS-waterworks

A Ruffus pipeline for Analysis of High-Throughput Sequencing data

mdos

MDOS motif discovery using orthologous sequences (alignment independent)

MixClone

A mixture model for inferring tumor subclonal populations

polyAcode

null

PyLOH

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

Rainfall

null

TEMT

Transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data (TEMT)

tree-hmm

Tree hidden Markov model for learning epigenetic states in multiple cell types