Campagne Laboratory's repositories
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 deep learning models trained with semi-simulation. See docs below for details.
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-like support for docker.
Editor2PDF
Provides a mechanism to render an MPS editor to PDF automatically.
GenotypeTensors
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
CloudInteractive
Companion project to NextflowWorkbench to help access Google Cloud storage in NW workflows and work interactively with data in the cloud.
genotype-dl-models
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.
gobyweb2-plugins
Plugin repository for GobyWeb 2.2+
variationanalysis-apps
DNANexus applications to process alignments and help develop or use neural-network based model callers.
XChart
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.
artifacts
Artifact manager for GobyWeb. Used by the GobyWeb plugins SDK.
Circles-meteor
Web front-end for the Circles project. Provides access to MPS nodes on the web.
CustomWebAspectExample
A detailed example of custom aspect for the MPS Language Workbench.
deeplearning4j
Deep Learning for Java, Scala & Clojure on Hadoop & Spark With GPUs - From Skymind
GobyWeb-Singularity
Singularity repo to package docker artifacts:base:latest container for running GobyWeb plugins with Singularity.
Metar_NW_Demo
Models for demo of MetaR and NextflowWorkbench
MPS_Model_Publishing
MPS side of the Circles project. Builds the MPS plugin that publishes models to the web app.
nyosh.core
NYoSh Core. Set of languages we reuse from the NYoSh workbench.
picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pytorch-adda
A PyTorch implementation for Adversarial Discriminative Domain Adaptation
stepslogger
Stepslogger tool, used by GobyWeb artifact manager to keep track of logs and show only the most relevant part when an error occurs.
Textractor
Textractor project, originally hosted at https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/textractor/, exported and imported into Git.
VdjcallerSingularity
singularity from docker