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antlr_mps

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

antrl_mps

Redirects to the correct repo

artifacts

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

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bdval

BDVal - Biomarker Development and Validation program

bdval_for_mps

This plugin provides a convenient way to configure and run BDVal projects. BDVal is a tool to facilitate the development and validation of predictive models from datasets with large number of features. For More information about BDVal, see http://bdval.campagnelab.org. First version of the BDVal MPS languages built by Victoria Benson.

buildsupport

Build scripts useful as a submodule

bwa

Burrow-Wheeler Aligner

circles-meteor

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

cloudinteractive

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

commandline

An annotation based command line parser

customwebaspectexample

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

debugrunconfigurations

a simple project to try to reproduce run configuration issues and help with debugging.

deeplearning4j

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

editor2pdf

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

flatbuffers

Maven artifacts containing compiled flatbuffers binaries and flatbuffers-java runtime library

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.

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

goby

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

goby3

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

gobyweb-plugins

Public repository for GobyWeb plugins

gobyweb-singularity

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

gobyweb2-plugins

Plugin repository for GobyWeb 2.2+

hts_compression_benchmark

Scripts and data to perform the compression benchmark described in Campagne et al PLOS 2013 (Compression of Structured High-Throughput Sequencing Data).

icb-ant-tasks

icb-stats

Stat package used across several Campagne lab projects

icb-utils

icb-utils shared by several Campagne lab projects

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

intellij-plugin-v4

An intellij plugin for ANTLR v4 in Intellij 12.1, 13.X

jetpad-mapper

JetBrains Jetpad Mapper Framework