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    33 repositories

    • arcasHLA

      Public
      Fast and accurate in silico inference of HLA genotypes from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •50•121•37•5•Updated Aug 20, 2024Aug 20, 2024

    • Pandora

      Public
      Microbial Signatures in Human RNAseq Data
      Python
      •
      MIT License
      •1•0•0•1•Updated Apr 22, 2024Apr 22, 2024

    • pitp

      Public
      HTML
      •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • Smoother

      Public
      A Unified and Modular Framework to Incorporate Structural Dependency in Spatial Omics Data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • ViromeOfManhattan

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • proscope

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Sep 22, 2023Sep 22, 2023

    • randomly

      Public
      A Library for Denoising Single-Cell Data with Random Matrix Theory
      sparsitydropoutdata-analysissingle-celldenoisingsingle-cell-rna-seqrandom-matrix-theorysingle-cell-analysissingle-cell-omics
      Jupyter Notebook
      •
      MIT License
      •10•36•2•0•Updated Aug 16, 2023Aug 16, 2023

    • INDEL-seq

      Public
      Scripts used for INDEL-seq data processing
      Python
      •0•0•0•0•Updated Jun 4, 2023Jun 4, 2023

    • randomlypage

      Public
      Webpage for randomly package
      HTML
      •1•0•0•0•Updated May 15, 2023May 15, 2023

    • spatial_dipg

      Public
      R
      •1•0•1•0•Updated Apr 21, 2023Apr 21, 2023

    • Chek2_scRNAseq

      Public
      The script used in manuscript "Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade" for scRNAseq data analysis.
      Jupyter Notebook
      •0•1•0•0•Updated Feb 8, 2023Feb 8, 2023

    • ES

      Public
      Python
      •2•0•0•0•Updated Jan 18, 2023Jan 18, 2023

    • randomlysite

      Public
      HTML
      •0•0•0•0•Updated Dec 5, 2022Dec 5, 2022

    • RabadanLab.github.io

      Public
      HTML
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • GBMsinglecell

      Public
      Python
      •0•0•0•0•Updated Aug 1, 2021Aug 1, 2021

    • PH_recombination_virus

      Public
      Pipeline to infer recombination rates
      R
      •0•1•0•0•Updated Mar 24, 2021Mar 24, 2021

    • Bootstrap-Analysis-Arriaga-Nature-Cancer-2020

      Public
      Script of bootstrap analysis of evolution tree used in Juan M Arriaga, et al. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nature Cancer (2020)
      R
      •0•2•0•0•Updated Aug 13, 2020Aug 13, 2020

    • TOBI

      Public
      TOBI predicts somatic variants from .vcf or .bam input
      R
      •
      MIT License
      •4•7•4•0•Updated May 29, 2019May 29, 2019

    • mutcomfocal

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated May 29, 2019May 29, 2019

    • dockersavi

      Public
      Dockerfolder for Docker-ized version of SAVI
      Dockerfile
      •1•0•0•0•Updated Feb 11, 2019Feb 11, 2019

    • pamler

      Public
      Shell
      •1•1•0•0•Updated Sep 10, 2018Sep 10, 2018

    • randomlyView

      Public
      HTML
      •0•0•0•0•Updated Jun 20, 2018Jun 20, 2018

    • mage-pipeline

      Public
      MAGE - Multilevel Analysis of Gene Expression
      R
      •
      MIT License
      •0•1•0•0•Updated Jan 6, 2018Jan 6, 2018

    • scTDA

      Public
      An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data
      Python
      •
      GNU General Public License v3.0
      •21•7•0•0•Updated Aug 10, 2017Aug 10, 2017

    • MITKats

      Public
      The Medical Imaging Interaction Toolkit with augmented tools for segmentation (MITKats), an extension of MITK with Threshold Components and Clipping Segmentation features.
      C++
      •
      Other
      •1•1•0•0•Updated May 18, 2017May 18, 2017

    • NORI

      Public
      NORI (Non-coding RNA Identification), a computational tool to identify lncRNAs using next generation sequencing.
      1•0•0•0•Updated Mar 15, 2017Mar 15, 2017

    • sakmapper

      Public
      Implementation of Mapper Algorithm
      Python
      •
      MIT License
      •10•1•0•0•Updated Nov 18, 2016Nov 18, 2016

    • EvoMod

      Public
      Evolutionary Moduli space visualization and statistics
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 27, 2016Oct 27, 2016

    • TARGet

      Public
      Topological inference of horizontal evolution from multiple sequence alignments
      C++
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Apr 22, 2016Apr 22, 2016

    • Pegasus

      Public
      Annotation and Prediction of Oncogenic Gene Fusions in RNAseq
      Java
      •
      MIT License
      •9•11•3•0•Updated Feb 20, 2016Feb 20, 2016