Repositories list

• HemaScribe

  Public
  HemaScribe: tools for analyzing single cell mouse hematopoiesis data

  R

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated May 29, 2025May 29, 2025

• arcasHLA

  Public
  Fast and accurate in silico inference of HLA genotypes from RNA-seq

  Python

  •

  GNU General Public License v3.0

  •58•142•42•9•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-analysis+ 6single-celldenoisingsingle-cell-rna-seqrandom-matrix-theorysingle-cell-analysissingle-cell-omics

  Jupyter Notebook

  •

  MIT License

  •10•37•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•8•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