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paddle

PArallel Distributed Deep LEarning

precisionfda

precisionFDA is a cloud based platform that provides an environment where the community can test, pilot, and benchmark new approaches to validating their next-generation sequencing (NGS) analysis pipelines. PrecisionFDA offers community members a secure and independent work area where, at their discretion, their bioinformatics tools or data can be kept private or shared with the precisionFDA participants.

primer_design

A Reliable and Flexible Multiplex PCR Primer Design Tool

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

radiant

Business analytics using R and Shiny. The radiant app combines the menus from radiant.data, radiant.design, radiant.basics, radiant.model, and radiant.multivariate.

rnaseq

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

sapshodt

Mass spectrometry (MS)-based proteomics analysis usually relies on database search. However, standard protein data-bases, such as NCBI-nr and Uniprot databases, don’t contain protein variants arising from SNPs that result in amino acid changes. Therefore, SAPshodt has been developed to introduce single amino acid polymorphism (SAP) information into an existing protein reference database on demand transmutator, enabling variant peptide detection in proteomics.

sars-cov-2_sequencing

stat479-machine-learning-fs18

Course material for STAT 479: Machine Learning (FS 2018) at University Wisconsin-Madison

tools-microbiome-analysis

A list of R environment based tools for marker gene microbiome data exploration, statistical analysis and visualization

ts

Torrent Suite

uxm_deconv

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies