@genepattern

GenePattern

A Platform for Reproducible Bioinformatics

Pinned repositories

  1. genepattern-notebook

    Platform for integrating genomic analysis with Jupyter Notebooks.

    JavaScript 18 5

  2. genepattern-server

    The GenePattern Server web application

    HTML 5 4

  3. genepattern-python

    GenePattern Python Library

    Python 2

  • Repo for the Hisat2 indexer module which creates indices for the Hisat2Aligner module

    Python Updated Oct 18, 2018
  • Repo for the dockerized Hisat 2 aligner module

    Python Updated Oct 18, 2018
  • Docker container and module wrapper for Amaretto from the Gavaert Lab at Stanford (http://med.stanford.edu/gevaertlab/software.html)

    R BSD-3-Clause Updated Oct 18, 2018
  • Docker container for hisat2 module

    Python 1 Updated Oct 17, 2018
  • Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)

    Python Updated Oct 13, 2018
  • common scripts for docker/aws batch containers used for GenePattern modules

    Shell Updated Oct 11, 2018
  • Docker build and module artifacts for community-amaretto module

    Updated Oct 10, 2018
  • The GenePattern Server web application

    HTML 5 4 Updated Oct 10, 2018
  • A framework for creating user-friendly widgets and tools in Jupyter Notebook.

    JavaScript 2 BSD-3-Clause Updated Oct 10, 2018
  • This repository contains the shared code used by the GenePattern modules.

    Updated Oct 9, 2018
  • Platform for integrating genomic analysis with Jupyter Notebooks.

    JavaScript 18 5 BSD-3-Clause Updated Oct 9, 2018
  • This module takes in a GDC manifest file, download the files listed on that manifest, and renames them to be human-friendly.

    Python 1 1 BSD-3-Clause Updated Oct 5, 2018
  • GenePattern Notebook Website

    HTML 1 Updated Oct 2, 2018
  • Python implementation of Gene Set Enrichment Analysis

    Python 2 BSD-3-Clause Updated Sep 18, 2018
  • R 1 1 BSD-3-Clause Updated Sep 18, 2018
  • GenePattern Python Library

    Python 2 BSD-3-Clause Updated Sep 17, 2018
  • 450k/EPIC methylation array based copy number variation analysis using GenePattern Notebooks.

    Jupyter Notebook BSD-3-Clause Updated Sep 14, 2018
  • Code used in the operation of the GenePattern Notebook Repository

    JavaScript 1 1 BSD-3-Clause Updated Sep 15, 2018
  • A wrapper module for the myvariant.info service

    Python BSD-3-Clause Updated Sep 11, 2018
  • Docker . module for the single cell toolkit

    Java 1 Updated Sep 11, 2018
  • CSS Updated Sep 10, 2018
  • R Updated Aug 22, 2018
  • R 1 1 Updated Aug 20, 2018
  • Docker . module for the single cell toolkit in R

    R BSD-3-Clause Updated Aug 21, 2018
  • Merges individial files containing HTSeq read counts into one file

    Python 4 1 Updated Aug 17, 2018
  • Dockerfiles supporting the GenePattern Notebook environment

    Dockerfile BSD-3-Clause Updated Aug 16, 2018
  • GenePattern Hierarchical Clustering module.

    Python 1 BSD-3-Clause Updated Aug 13, 2018
  • These are the GenePattern notebooks in which TCGAImporter is used to generate different datasets

    Jupyter Notebook BSD-3-Clause Updated Aug 8, 2018
  • GenePattern docker container for the download from gdc module

    Python Updated Aug 7, 2018
  • Jupyter Notebook 2 4 BSD-3-Clause Updated Aug 3, 2018