Repositories list

• GenotypeTensors

  Public
  This project provides tools to load the vectorized genotype information files (.vec/.vecp) produced with goby3 and variation analysis. It also demonstrates how to train deep-learning models using information in these files with pytorch.LICENSE

  Python

  •

  MIT License

  •1•7•0•0•Updated Nov 20, 2018Nov 20, 2018

• torchfold

  Public
  Tools for PyTorch

  Python

  •

  Apache License 2.0

  •28•1•0•0•Updated Aug 2, 2018Aug 2, 2018

• variationanalysis-apps

  Public
  DNANexus applications to process alignments and help develop or use neural-network based model callers.

  Shell

  •

  MIT License

  •1•1•0•0•Updated Jun 27, 2018Jun 27, 2018

• variationanalysis

  Public
  This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate deep learning models trained with semi-simulation. See docs below for details.

  Java

  •

  Other

  •20•50•0•0•Updated Jun 1, 2018Jun 1, 2018

• goby3

  Public
  Releases 3.+ of the Goby High-throughput sequencing framework and tools.

  Java

  •

  Other

  •2•5•9•0•Updated Jun 1, 2018Jun 1, 2018

• Editor2PDF

  Public
  Provides a mechanism to render an MPS editor to PDF automatically.

  Java

  •

  GNU Affero General Public License v3.0

  •2•10•2•0•Updated May 24, 2018May 24, 2018

• pytorch-adda

  Public
  A PyTorch implementation for Adversarial Discriminative Domain Adaptation

  Python

  •

  MIT License

  •140•0•0•0•Updated Apr 24, 2018Apr 24, 2018

• gobyweb2-plugins

  Public
  Plugin repository for GobyWeb 2.2+

  Perl

  •

  Apache License 2.0

  •1•1•0•0•Updated Mar 4, 2018Mar 4, 2018

• GobyWeb-Singularity

  Public
  Singularity repo to package docker artifacts:base:latest container for running GobyWeb plugins with Singularity.

  Shell

  •0•0•0•0•Updated Jan 19, 2018Jan 19, 2018

• picard

  Public
  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

  Java

  •

  MIT License

  •369•0•0•0•Updated Jan 12, 2018Jan 12, 2018

• genotype-dl-models

  Public
  A repository of deep learning genotype models. Trained with the variationanalysis project, these models can be loaded and used by goby3 to call somatic variations of germline genotypes in sequencing data. The repository will accept pull requests with models for specific assays, platforms or analysis protocols.

  0•1•0•0•Updated Nov 14, 2017Nov 14, 2017

• ANTLR_MPS

  Public
  An ANTLR language for MPS, and the ToMPS language to help create MPS languages and ANTRL visitors from an ANTLR 4 grammar.

  Java

  •

  Other

  •8•25•4•0•Updated Sep 6, 2017Sep 6, 2017

• nyosh.core

  Public
  NYoSh Core. Set of languages we reuse from the NYoSh workbench.

  Java

  •

  Other

  •0•0•0•0•Updated Sep 6, 2017Sep 6, 2017

• stepslogger

  Public
  Stepslogger tool, used by GobyWeb artifact manager to keep track of logs and show only the most relevant part when an error occurs.

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 29, 2017Aug 29, 2017

• artifacts

  Public
  Artifact manager for GobyWeb. Used by the GobyWeb plugins SDK.

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 29, 2017Aug 29, 2017

• XChart

  Public
  An MPS wrapper around XChart (https://github.com/timmolter/XChart). Makes it possible to preview charts constructed from data in TSV and other delimited text files, and to produce an implementation of the charts that can display the content of new files with similar columns.

  Java

  •

  Other

  •1•1•0•0•Updated Aug 2, 2017Aug 2, 2017

• MetaR

  Public
  Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name.

  Java

  •

  Other

  •5•51•14•0•Updated Jun 24, 2017Jun 24, 2017

• VdjcallerSingularity

  Public
  singularity from docker

  0•0•0•0•Updated Jun 19, 2017Jun 19, 2017

• deeplearning4j

  Public
  Deep Learning for Java, Scala & Clojure on Hadoop & Spark With GPUs - From Skymind

  Java

  •

  Apache License 2.0

  •3.8k•0•0•0•Updated Apr 14, 2017Apr 14, 2017

• Textractor

  Public
  Textractor project, originally hosted at https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/textractor/, exported and imported into Git.

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 27, 2017Feb 27, 2017

• Metar_NW_Demo

  Public
  Models for demo of MetaR and NextflowWorkbench

  Apache License 2.0

  •0•0•0•0•Updated Oct 22, 2016Oct 22, 2016

• JSAP

  Public
  A fork of the JSAP project (http://www.martiansoftware.com/jsap/) modified by our lab to work with Java 1.7+.

  Java

  •

  Other

  •0•0•0•0•Updated Oct 2, 2016Oct 2, 2016

• icb-utils

  Public
  icb-utils shared by several Campagne lab projects

  Java

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Oct 2, 2016Oct 2, 2016

• NextflowWorkbench

  Public
  An implementation of Nextflow.io with Language Workbench Technology. The project helps create computational pipelines that run with the Nextflow.io middleware. Includes dockerfile language and IDE-like support for docker.

  Java

  •

  Other

  •4•22•4•0•Updated Aug 9, 2016Aug 9, 2016

• CloudInteractive

  Public
  Companion project to NextflowWorkbench to help access Google Cloud storage in NW workflows and work interactively with data in the cloud.

  Shell

  •

  Other

  •0•1•0•0•Updated Aug 9, 2016Aug 9, 2016

• nd4j

  Public
  Fast, Scientific and Numerical Computing for the JVM (NDArrays)

  Java

  •

  Apache License 2.0

  •508•0•0•0•Updated Aug 8, 2016Aug 8, 2016

• goby

  Public
  Goby framework and tools for analysis of high-throughput sequencing data

  Java

  •

  Other

  •2•17•2•0•Updated Jun 21, 2016Jun 21, 2016

• Circles-meteor

  Public
  Web front-end for the Circles project. Provides access to MPS nodes on the web.

  JavaScript

  •

  Apache License 2.0

  •1•0•0•0•Updated May 23, 2016May 23, 2016

• MPS_Model_Publishing

  Public
  MPS side of the Circles project. Builds the MPS plugin that publishes models to the web app.

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated May 12, 2016May 12, 2016

• CustomWebAspectExample

  Public
  A detailed example of custom aspect for the MPS Language Workbench.

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 18, 2016Apr 18, 2016