Skip to content

@ucsd-ccbb UC San Diego Center for Computational Biology & Bioinformatics

All

    Repositories list

    24 repositories

    • NetColoc

      Public
      development of network co-localization tool
      Jupyter Notebook
      •
      MIT License
      •8•18•2•0•Updated Sep 21, 2026Sep 21, 2026

    • SLC22_TCGA_Methods

      Public archive
      Whisenant/Nigam TCGA/SLC22 Analysis
      Jupyter Notebook
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

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

      Public archive
      Jupyter Notebook
      •0•1•0•0•Updated Jul 23, 2025Jul 23, 2025

    • 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

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

    • visJS2jupyter

      Public
      visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells
      Jupyter Notebook
      •
      MIT License
      •16•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…
      sequencingepidemiologyviral-genomics
      sequencingepidemiologyviral-genomics
      Python
      •
      MIT License
      •2•11•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•3•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

    • VAPr

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

    • Ward_scRNAseq_2019

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

    • qiimp

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

    • mali-dual-crispr-pipeline

      Public archive
      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…
      Python
      •
      MIT License
      •2•4•0•0•Updated Oct 3, 2017Oct 3, 2017

    • jupyter-pathway

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

    • ccbb-ucsd-pyutils

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

    • Oncolist

      Public archive
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2016Sep 23, 2016
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.