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    39 repositories

    • esm-efficient

      Public
      Python
      •1•21•1•0•Updated Oct 28, 2024Oct 28, 2024

    • EpiOut

      Public
      A statistical method to detect, analyze and visualize aberrations in chromatin accessibility (ATAC-seq, DNase-Seq) and quantify its effect on gene expression.
      Python
      •0•2•1•0•Updated Mar 6, 2024Mar 6, 2024

    • UFold

      Public
      Python
      •
      MIT License
      •29•59•25•0•Updated Nov 27, 2023Nov 27, 2023

    • BioML

      Public
      MIT License
      •2•5•0•1•Updated Feb 15, 2023Feb 15, 2023

    • scFAN

      Public
      Python
      •
      MIT License
      •1•3•0•0•Updated Oct 14, 2022Oct 14, 2022

    • SAILERX

      Public
      Jupyter Notebook
      •0•3•1•0•Updated Jul 3, 2022Jul 3, 2022

    • Video-Pre-Training

      Public
      Video PreTraining (VPT): Learning to Act by Watching Unlabeled Online Videos
      Python
      •
      MIT License
      •145•0•0•0•Updated Jun 25, 2022Jun 25, 2022

    • RP-Net

      Public
      Code for Recurrent Mask Refinement for Few-Shot Medical Image Segmentation (ICCV 2021).
      Python
      •9•57•8•0•Updated Aug 28, 2021Aug 28, 2021

    • SAILER

      Public
      Jupyter Notebook
      •
      MIT License
      •3•5•1•0•Updated Jul 27, 2021Jul 27, 2021

    • NoduleNet

      Public
      [MICCAI' 19] NoduleNet: Decoupled False Positive Reduction for Pulmonary Nodule Detection and Segmentation
      Python
      •
      Other
      •58•189•22•0•Updated Jun 24, 2020Jun 24, 2020

    • FactorNet

      Public
      A deep learning package for predicting TF binding
      Python
      •
      MIT License
      •11•41•3•0•Updated Jan 23, 2020Jan 23, 2020

    • UaNet

      Public
      Jupyter Notebook
      •
      Other
      •18•59•6•0•Updated Dec 17, 2019Dec 17, 2019

    • DeepLung

      Public
      WACV18 paper "DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification"
      Python
      •
      GNU General Public License v3.0
      •53•153•2•0•Updated Sep 8, 2019Sep 8, 2019

    • D-GEX

      Public
      Deep learning for gene expression inference
      deep-learninggene-expression
      Python
      •
      GNU General Public License v2.0
      •57•147•0•0•Updated Feb 18, 2019Feb 18, 2019

    • DeepEM-for-Weakly-Supervised-Detection-1

      Public
      MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection
      Jupyter Notebook
      •17•17•0•0•Updated Jan 16, 2019Jan 16, 2019

    • DeepEM-for-Weakly-Supervised-Detection

      Public
      MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection
      Apache License 2.0
      •3•15•0•0•Updated Jul 22, 2018Jul 22, 2018

    • EXTREME

      Public
      An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data
      C
      •
      GNU General Public License v2.0
      •4•30•0•0•Updated May 22, 2018May 22, 2018

    • ChestXRay

      Public
      Jupyter Notebook
      •0•5•1•0•Updated Apr 13, 2018Apr 13, 2018

    • HLA-bind

      Public
      Amino acid embedding and Convolutional Neural Network for HLA Class I-peptide binding prediction
      Python
      •
      MIT License
      •14•25•1•0•Updated Aug 3, 2017Aug 3, 2017

    • PyLOH

      Public
      Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
      Python
      •
      GNU General Public License v2.0
      •15•38•2•0•Updated Jul 19, 2017Jul 19, 2017

    • DeepCons

      Public
      Understanding sequence conservation with deep learning
      HTML
      •
      GNU General Public License v3.0
      •7•19•0•0•Updated Mar 19, 2017Mar 19, 2017

    • CoreNLP

      Public
      Stanford CoreNLP: A Java suite of core NLP tools.
      Java
      •
      GNU General Public License v3.0
      •2.7k•0•0•0•Updated Mar 8, 2017Mar 8, 2017

    • RBPnet

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 10, 2017Feb 10, 2017

    • DanQ

      Public
      A hybrid convolutional and recurrent neural network for predicting the function of DNA sequences
      Groff
      •
      Other
      •71•157•3•0•Updated Jan 14, 2017Jan 14, 2017

    • ConsDEEP

      Public
      Sequence conservatoin analysis with deep learning
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 21, 2016Jul 21, 2016

    • MixClone

      Public
      A mixture model for inferring tumor subclonal populations
      Python
      •
      GNU General Public License v2.0
      •4•5•0•0•Updated Jul 16, 2016Jul 16, 2016

    • TEMT

      Public
      Transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data (TEMT)
      Python
      •
      Artistic License 2.0
      •5•5•0•0•Updated Apr 26, 2016Apr 26, 2016

    • ChromDEEP

      Public
      Chromatin states analysis with deep learning
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Mar 2, 2016Mar 2, 2016

    • genomix

      Public
      Parallel genome assembly using Hyracks
      Java
      •2•3•22•2•Updated Feb 22, 2016Feb 22, 2016

    • DEEMOL

      Public
      Deep learning for molecular modelling
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 12, 2016Feb 12, 2016