XIE LAB @ UCI (@uci-cbcl)
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Top repositories

1

NoduleNet

[MICCAI' 19] NoduleNet: Decoupled False Positive Reduction for Pulmonary Nodule Detection and Segmentation
Python
187
star
2

DanQ

A hybrid convolutional and recurrent neural network for predicting the function of DNA sequences
Groff
157
star
3

DeepLung

WACV18 paper "DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification"
Python
153
star
4

D-GEX

Deep learning for gene expression inference
Python
146
star
5

UFold

Python
59
star
6

UaNet

Jupyter Notebook
59
star
7

RP-Net

Code for Recurrent Mask Refinement for Few-Shot Medical Image Segmentation (ICCV 2021).
Python
56
star
8

FactorNet

A deep learning package for predicting TF binding
Python
41
star
9

PyLOH

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
Python
38
star
10

EXTREME

An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data
C
30
star
11

tree-hmm

Tree hidden Markov model for learning epigenetic states in multiple cell types
Python
27
star
12

HLA-bind

Amino acid embedding and Convolutional Neural Network for HLA Class I-peptide binding prediction
Python
25
star
13

DeepCons

Understanding sequence conservation with deep learning
HTML
19
star
14

DeepEM-for-Weakly-Supervised-Detection

MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection
15
star
15

GBMCI

The implementation of gradient boosting machine for concordance index learning.
C++
14
star
16

esm-efficient

Python
12
star
17

SAILER

Jupyter Notebook
5
star
18

BioML

5
star
19

TEMT

Transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data (TEMT)
Python
5
star
20

ChestXRay

Jupyter Notebook
5
star
21

MixClone

A mixture model for inferring tumor subclonal populations
Python
5
star
22

SAILERX

Jupyter Notebook
3
star
23

scFAN

Python
3
star
24

genomix

Parallel genome assembly using Hyracks
Java
3
star
25

EpiOut

A statistical method to detect, analyze and visualize aberrations in chromatin accessibility (ATAC-seq, DNase-Seq) and quantify its effect on gene expression.
Python
2
star
26

Rainfall

MATLAB
1
star
27

RBPnet

Python
1
star