@CampagneLaboratory

Campagne Laboratory

Pinned repositories

  1. variationanalysis

    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 de…

    Java 42 19

  2. MetaR

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

    Java 39 4

  3. NextflowWorkbench

    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-…

    Java 18 4

  4. ANTLR_MPS

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

    Java 15 3

  5. Editor2PDF

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

    Java 6 1

  6. goby3

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

    Java 5 1

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

    Shell 1 MIT Updated Jun 22, 2018
  • 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 6 1 MIT Updated Jun 2, 2018
  • 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 42 19 Updated Jun 1, 2018
  • Releases 3.+ of the Goby High-throughput sequencing framework and tools.

    Java 5 1 Updated Jun 1, 2018
  • Provides a mechanism to render an MPS editor to PDF automatically.

    Java 6 1 AGPL-3.0 Updated May 24, 2018
  • A PyTorch implementation for Adversarial Discriminative Domain Adaptation

    Python 26 MIT Updated Apr 24, 2018
  • Plugin repository for GobyWeb 2.2+

    Perl 1 1 Apache-2.0 Updated Mar 4, 2018
  • Singularity repo to package docker artifacts:base:latest container for running GobyWeb plugins with Singularity.

    Shell Updated Jan 19, 2018
  • 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 237 MIT Updated Jan 12, 2018
  • 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.

    1 Updated Nov 14, 2017
  • An ANTLR language for MPS, and the ToMPS language to help create MPS languages and ANTRL visitors from an ANTLR 4 grammar.

    Java 15 3 Updated Sep 6, 2017
  • NYoSh Core. Set of languages we reuse from the NYoSh workbench.

    Java Updated Sep 6, 2017
  • 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-2.0 Updated Aug 29, 2017
  • Artifact manager for GobyWeb. Used by the GobyWeb plugins SDK.

    Java Apache-2.0 Updated Aug 29, 2017
  • 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 Updated Aug 2, 2017
  • Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name.

    Java 39 4 Updated Jun 24, 2017
  • singularity from docker

    Updated Jun 19, 2017
  • Deep Learning for Java, Scala & Clojure on Hadoop & Spark With GPUs - From Skymind

    Java 4,310 Apache-2.0 Updated Apr 14, 2017
  • Textractor project, originally hosted at https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/textractor/, exported and imported into Git.

    HTML GPL-3.0 Updated Feb 27, 2017
  • Models for demo of MetaR and NextflowWorkbench

    Apache-2.0 Updated Oct 22, 2016
  • A fork of the JSAP project (http://www.martiansoftware.com/jsap/) modified by our lab to work with Java 1.7+.

    Java Updated Oct 2, 2016
  • icb-utils shared by several Campagne lab projects

    Java 1 GPL-3.0 Updated Oct 2, 2016
  • 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 18 4 Updated Aug 9, 2016
  • Companion project to NextflowWorkbench to help access Google Cloud storage in NW workflows and work interactively with data in the cloud.

    Shell 1 Updated Aug 9, 2016
  • Fast, Scientific and Numerical Computing for the JVM (NDArrays)

    Java 515 Apache-2.0 Updated Aug 8, 2016
  • Goby framework and tools for analysis of high-throughput sequencing data

    Java 17 1 Updated Jun 21, 2016
  • Web front-end for the Circles project. Provides access to MPS nodes on the web.

    JavaScript 1 Apache-2.0 Updated May 23, 2016
  • MPS side of the Circles project. Builds the MPS plugin that publishes models to the web app.

    Java Apache-2.0 Updated May 12, 2016
  • A detailed example of custom aspect for the MPS Language Workbench.

    Java Apache-2.0 Updated Apr 18, 2016
  • Redirects to the correct repo

    Updated Apr 5, 2016