Repositories list

• sCRAP_CommandLine

  Public
  selective Cross Reactive Antigen Presentation (command line version)

  R

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  Other

  •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

• sCRAP

  Public
  selective Cross Reactive Antigen Presentation

  R

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  Other

  •0•1•0•0•Updated Feb 12, 2024Feb 12, 2024

• mosse-lab-tools

  Public
  Various QoL tools and script snippets to aid researchers in the Mosse lab

  MIT License

  •0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

• pptc-pdx-ethnicity-inference

  Public
  Ethnicity inference for Pediatric Preclinical Testing Consortium (PPTC) patient-derived xenograft models

  R

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  BSD 3-Clause "New" or "Revised" License

  •3•0•0•0•Updated Oct 28, 2021Oct 28, 2021

• immunoprofile_shinyapp

  Public
  Shiny app for immunoprofiling across pediatric and adult tumors

  R

  •0•0•0•0•Updated Mar 24, 2020Mar 24, 2020

• epigenomics-data-descriptor

  Public
  Shell

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  BSD 3-Clause "New" or "Revised" License

  •0•4•0•0•Updated Mar 9, 2020Mar 9, 2020

• pptc-pdx-copy-number-and-SVs

  Public
  Indel and Breakpoints plots

  R

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 27, 2019Dec 27, 2019

• create-pptc-pdx-oncoprints

  Public
  As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of …

  classifierclusteringfusion+ 4rna-sequencingethnicity-analysisexome-sequencingmutational-signatures

  R

  •2•3•0•0•Updated Dec 11, 2019Dec 11, 2019

• pptc-pdx-tmb

  Public
  R

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Sep 22, 2019Sep 22, 2019

• pptc-pdx-classifier-analysis

  Public
  R

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Sep 22, 2019Sep 22, 2019

• gmkf-nbl-fusion-analysis

  Public
  Fusion analysis for GMKF Neuroblastoma

  R

  •0•0•0•0•Updated Sep 3, 2019Sep 3, 2019

• pptc-pdx-RNA-Seq-clustering

  Public
  HTML

  •0•0•1•0•Updated Aug 30, 2019Aug 30, 2019

• create-pptc-pdx-pie

  Public
  Pie chart for Figure 1 of Manuscript

  R

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 2, 2019Aug 2, 2019

• pptx-pdx-fusion-analysis

  Public
  Fusion pipeline and figures

  R

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  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Jul 26, 2019Jul 26, 2019

• pdx-classification

  Public
  Applying Machine Learning Ras, NF1, and TP53 Classifiers to PDX model gene expression

  machine-learninggene-expressioncancer-genomics+ 6pdxpediatric-cancerclassifiercancer-genome-atlasmachine-learning-rasras-activation

  HTML

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  BSD 3-Clause "New" or "Revised" License

  •1•3•0•0•Updated Jul 9, 2019Jul 9, 2019

• create-pptc-pdx-corplots

  Public
  R

  •1•2•0•0•Updated Jul 7, 2019Jul 7, 2019

• maftools

  Public
  Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

  R

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  MIT License

  •223•0•0•0•Updated Jul 6, 2019Jul 6, 2019

• pptc-pdx-mut-sigs

  Public
  R

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  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Apr 15, 2019Apr 15, 2019

• pdx-mouse-subtraction

  Public
  Python

  •0•4•0•0•Updated Mar 12, 2019Mar 12, 2019

• NBL-cell-line-RNA-seq

  Public
  R

  •1•2•0•0•Updated Feb 22, 2019Feb 22, 2019

• tad_pathways_pipeline

  Public
  Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

  Python

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  MIT License

  •5•0•0•0•Updated Dec 18, 2018Dec 18, 2018