Discover ucsd-ccbb/C-VIEW Open Source project

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Language
Python
License
MIT License
Created almost 4 years ago
Updated over 1 year ago

ucsd-ccbb

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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.

visJS2jupyter

visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells

Jupyter Notebook

VAPr

VAPr: A Python package for NoSQL variant data storage, annotation and prioritization

Python

NetColoc

development of network co-localization tool

Jupyter Notebook

cirrus-ngs

Python

gsia

Gene Set Information Analysis

jupyter-pathway

Canonical pathway visualization and analysis

Jupyter Notebook

mali-dual-crispr-pipeline

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 California, San Diego.

Python

qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints

Python

ASD_combined_network_analysis

Notebooks from ASD-CHD combined network analysis paper

Jupyter Notebook

MPN_atlas_methods

Source code for methods for A Dynamic Pre-Leukemia Stem Cell Atlas of Myeloproliferative Neoplasm Evolution

Jupyter Notebook

network_bio_toolkit

toolbox of network biology methods

Jupyter Notebook

shinyGWAS

visualization for GWAS. Mostly based on outputs from FUMA

Jupyter Notebook

ucsd-ccbb/C-VIEW

ucsd-ccbb

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