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DNANexus applications to process alignments and help develop or use neural-network based model callers.
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
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.
Releases 3.+ of the Goby High-throughput sequencing framework and tools.
Provides a mechanism to render an MPS editor to PDF automatically.
A PyTorch implementation for Adversarial Discriminative Domain Adaptation
Plugin repository for GobyWeb 2.2+
Singularity repo to package docker artifacts:base:latest container for running GobyWeb plugins with Singularity.
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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.
An ANTLR language for MPS, and the ToMPS language to help create MPS languages and ANTRL visitors from an ANTLR 4 grammar.
NYoSh Core. Set of languages we reuse from the NYoSh workbench.
Stepslogger tool, used by GobyWeb artifact manager to keep track of logs and show only the most relevant part when an error occurs.
Artifact manager for GobyWeb. Used by the GobyWeb plugins SDK.
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.
Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name.
singularity from docker
Deep Learning for Java, Scala & Clojure on Hadoop & Spark With GPUs - From Skymind
Textractor project, originally hosted at https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/textractor/, exported and imported into Git.
Models for demo of MetaR and NextflowWorkbench
A fork of the JSAP project (http://www.martiansoftware.com/jsap/) modified by our lab to work with Java 1.7+.
icb-utils shared by several Campagne lab projects
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.
Companion project to NextflowWorkbench to help access Google Cloud storage in NW workflows and work interactively with data in the cloud.
Fast, Scientific and Numerical Computing for the JVM (NDArrays)
Goby framework and tools for analysis of high-throughput sequencing data
Web front-end for the Circles project. Provides access to MPS nodes on the web.
MPS side of the Circles project. Builds the MPS plugin that publishes models to the web app.
A detailed example of custom aspect for the MPS Language Workbench.
Redirects to the correct repo