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arem

AREM -- Aligning Reads by Expectation-Maximization

bioml

chestxray

chromdeep

Chromatin states analysis with deep learning

consdeep

Sequence conservatoin analysis with deep learning

consensus-search

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

corenlp

Stanford CoreNLP: A Java suite of core NLP tools.

d-gex

Deep learning for gene expression inference

danq

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

deemol

Deep learning for molecular modelling

deepcadd

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

deepem-for-weakly-supervised-detection-1

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"

epiout

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

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

nodulenet

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

polyacode

pyloh

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

rainfall

rbpnet

rp-net

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