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    26 repositories

    • NetColoc

      Public
      development of network co-localization tool
      Jupyter Notebook
      •
      MIT License
      •6•14•3•0•Updated Oct 21, 2024Oct 21, 2024

    • ASD_combined_network_analysis

      Public
      Notebooks from ASD-CHD combined network analysis paper
      Jupyter Notebook
      •
      MIT License
      •1•2•1•0•Updated Jun 20, 2024Jun 20, 2024

    • Friedman_WGS

      Public
      Shell
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • SBR_temp_bcbio

      Public
      0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • MitoProteomicsMethods

      Public archive
      Mitochondrial Proteomic Analysis for Yu/Pekkurnaz Project
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 3, 2024May 3, 2024

    • trem2_sRNAseq

      Public
      analysis of scRNAseq for Trem2 paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 21, 2024Mar 21, 2024

    • VK2-vaginal-epithelial-cell-RNA-seq-analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 9, 2023Oct 9, 2023

    • visJS2jupyter

      Public
      visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells
      Jupyter Notebook
      •
      MIT License
      •17•78•7•2•Updated Aug 15, 2023Aug 15, 2023

    • C-VIEW

      Public
      This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
      sequencingepidemiologyviral-genomics
      Python
      •
      MIT License
      •2•10•22•0•Updated Aug 1, 2023Aug 1, 2023

    • pAML_StemCell_Methods

      Public
      All computational code for execution of analyses described in Methods
      Jupyter Notebook
      •0•0•0•0•Updated Jan 24, 2023Jan 24, 2023

    • MPN_atlas_methods

      Public
      Source code for methods for A Dynamic Pre-Leukemia Stem Cell Atlas of Myeloproliferative Neoplasm Evolution
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 20, 2023Jan 20, 2023

    • shinyGWAS

      Public
      visualization for GWAS. Mostly based on outputs from FUMA
      Jupyter Notebook
      •0•2•7•0•Updated Aug 17, 2022Aug 17, 2022

    • SLC22_TCGA_Methods

      Public archive
      Whisenant/Nigam TCGA/SLC22 Analysis
      Jupyter Notebook
      •0•0•0•0•Updated Aug 17, 2022Aug 17, 2022

    • VAPr

      Public
      VAPr: A Python package for NoSQL variant data storage, annotation and prioritization
      Python
      •
      MIT License
      •3•36•9•0•Updated Jun 30, 2021Jun 30, 2021

    • education

      Public
      0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • Ward_scRNAseq_2019

      Public
      Code for BMAC single cell RNAseq analysis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2021Mar 11, 2021

    • cirrus-ngs

      Public
      Python
      •
      MIT License
      •3•8•14•0•Updated May 30, 2020May 30, 2020

    • netprop_zscore

      Public
      calculate network propagation z-score, with degree matched null model
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2020Jan 16, 2020

    • network_bio_toolkit

      Public
      toolbox of network biology methods
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 9, 2018Nov 9, 2018

    • qiimp

      Public
      Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
      Python
      •7•3•49•0•Updated Nov 1, 2018Nov 1, 2018

    • gsia

      Public
      Gene Set Information Analysis
      R
      •1•7•4•1•Updated Aug 28, 2018Aug 28, 2018

    • crispr_network_analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 26, 2018Apr 26, 2018

    • mali-dual-crispr-pipeline

      Public
      This repository contains code for the dual-CRISPR screen analysis pipeline developed to analyze results from the dual-CRISPR screening system set up by the labs of Dr. Prashant Mali and Dr. Trey Ideker. The software is developed by Amanda Birmingham and Roman Sasik of the Center for Computational Biology and Bioinformatics at the University of C…
      Python
      •
      MIT License
      •2•4•4•0•Updated Oct 3, 2017Oct 3, 2017

    • jupyter-pathway

      Public
      Canonical pathway visualization and analysis
      Jupyter Notebook
      •
      MIT License
      •2•5•0•0•Updated Jun 9, 2017Jun 9, 2017

    • ccbb-ucsd-pyutils

      Public
      Python utilities for general use at CCBB
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 25, 2017Apr 25, 2017

    • Oncolist

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2016Sep 23, 2016