Displaying 1 to 20 from 39 results

deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

  •    Python

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.DeepVariant is a suite of Python/C++ programs that run on any Unix-like operating system. For convenience the documentation refers to building and running DeepVariant on Google Cloud Platform, but the tools themselves can be built and run on any standard Linux computer, including on-premise machines. Note that DeepVariant currently requires Python 2.7 and does not yet work with Python 3.

galaxy - Data intensive science for everyone.

  •    Python

You may wish to make changes from the default configuration. This can be done in the config/galaxy.ini file. Note that not all dependencies for the tools provided in the tool_conf.xml.sample are included. To install them please visit "Manage dependencies" in the admin interface.

gibber - An audiovisual live coding environment for the browser

  •    Javascript

Gibber is a live coding environment for the web browser, using the Gibberish.js audio engine, the CodeMirror code editor library and wrapping Three.js for 3d graphics and shader support. Version 2 of Gibber features a much more efficient audio engine, some interesting mapping abstractions and a server/database backend for publishing and browsing files and collaboratively live coding. In order of preference, Gibber runs in Chrome, Safari, and Firefox. The current public URL for the Gibber environment is http://gibber.mat.ucsb.edu. Below is a code sample that shows off the mapping abstractions in Gibber by mapping the output envelope of various drum sounds to the rotation of a Cube and a shader uniform.

OTTO - Your entire music-making workflow, in one box.

  •    C++

The OTTO is a complete hardware and software solution, with synths, a sampler, effects, sequencers, and studio modules. The interface is modal, easy to use, simple, but most of all, it encourages experimentation. The graphics are quirky, and the workflow is minimal. Yes, the OTTO is heavily inspired by the OP-1, but it is not an OP-1 clone. If you want an OP-1 you can get it here.

gatk - Official code repository for GATK versions 4 and up

  •    Java

Please see the GATK website, where you can download a precompiled executable, read documentation, ask questions, and receive technical support. This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents of this repository are 100% open source and released under the BSD 3-Clause license (see LICENSE.TXT).

fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

  •    C++

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. By default, the HTML report is saved to fastp.html (can be specified with -h option), and the JSON report is saved to fastp.json (can be specified with -j option).

Mutation Explorer


In-Del detection program from Sanger sequencing data

fetch - Simple & Efficient data access for Scala and Scala.js

  •    Scala

Add the following dependency to your project's build file.Fetch is a library for making access to data both simple & efficient. Fetch is especially useful when querying data that has a latency cost, such as databases or web services.

temporal - Non-blocking, temporal task sequencing. For use with robots built with Johnny-Five

  •    Javascript

Non-blocking, temporal task sequencing. temporal does NOT use setTimeout or setInterval, however there is a cost for using "recursive" setImmediate to create an extremely fast, async execution loop. CPU usage is expected to peak when using temporal, because the internal ticker needs to execute as fast as possible and as many times per second as possible. It's this speed that allows temporal to review the internal schedule for tasks to execute more than once per millisecond, which is needed to create preferential execution cycles for hardware programming.temporal is not good for sparse task scheduling.

ngCGH - Tools for producing pseudo-cgh of next-generation sequencing data

  •    Python

Next-generation sequencing of tumor/normal pairs provides a good opportunity to examine large-scale copy number variation in the tumor relative to the normal sample. In practice, this concept seems to extend even to exome-capture sequencing of pairs of tumor and normal. This library consists of a single script, ngCGH, that computes a pseudo-CGH using simple coverage counting on the tumor relative to the normal. I have chosen to use a fixed number of reads in the normal sample as the "windowing" approach. This has the advantage of producing copy number estimates that should have similar variance at each location. The algorithm will adaptively deal with inhomogeneities across the genome such as those associated with exome-capture technologies (to the extent that the capture was similar in both tumor and normal). The disadvantage is that the pseudo-probes will be at different locations for every "normal control" sample.

gibber.audio.lib - music and audio library for Gibber

  •    Javascript

This library provides the audio capabilities of Gibber without the code editing environment. The build outputs a UMD file, gibber.audio.lib.js, and a minified version.


  •    Javascript

This library provides the graphics and audio capabilities of Gibber without the code editing environment. The build outputs a UMD file, gibber.lib.js, and a minified version.

p5.gibber.js - Music and audio programming for p5.js

  •    Javascript

Music and audio programming for p5.js. This is a thin wrapper around Gibber.lib, which enables easy musical sequencing and audio signal processing. There are a variety of examples in the included examples directory.

nanotunes - A small music format and an accompanying implementation using OscillatorNode

  •    Javascript

NanoTunes is a small schema for structuring music. This repository includes a JavaScript implementation, built upon OscillatorNode. Developers must shape their own sounds; NanoTunes is simply a means of representing the notes that should be played, and for how long per bar.

defaultxrs-pd-abstractions - a set of abstractions written for pure data, including sequencers, guis, and other utilties


This is a collection of abstractions I've made for Pure Data. It includes sequencers, GUIs, general utilities, and a few effects and synths. I'm still in the process of writing them, so consider them "beta", and expect changes if you upgrade later (which will hopefully be mentioned in commit messages). Some objects might get renamed, removed, or end up working/looking completely different later. Beware of this. Right now, most of these abstractions will probably only work under Pd-extended 0.43. Since Pd-extended is no longer maintained, I'll slowly be working towards Pd-vanilla compatibility for this library.

galaxy-rna-workbench - Galaxy RNA workbench

  •    HTML

The RNA Galaxy workbench is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge. The current implementation comprises more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction.

beet.js - Polyrhythmic Sequencer library for Web Audio API.

  •    Javascript

Polyrhythmic Sequencer library for Web Audio API. The sequencer can have multiple layers where each layer has a different step count. This feature allows the user to create complex polyrhythms and euclidean rhythms using a simple api.

catch - A package for designing compact and comprehensive probe sets.

  •    Python

CATCH is a Python package for designing probe sets to use in hybrid capture experiments. Installing CATCH with pip, as described below, will install NumPy and SciPy if they are not already installed.

InSilicoSeq - :rocket: A sequencing simulator

  •    Python

InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.