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This is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)
akutils with massive updates over v1.1 to functionality and command line interface.
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GrCH37 reference sequence and one or more regions of interest. This is development version. Please "watch" this repository for production release and methods manuscript soon.
Deep Learning examples with Keras.
Incubator for useful bioinformatics code, primarily in Python and R
Bioinformatics tools
Notes on Scientific Computing for Biomechanics and Motor Control
Development and validation of an interpretable deep learning framework for Alzheimer's disease classification
A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.
R code for the algorithm used in Cohen et al. Science 2018 "Detection and localization of surgically resectable cancers with a multi-analyte blood test", Science 2018, 359(6378):926-930.
Applied Neural Networks to Johns Hopkins' CancerSEEK blood test data for early detection of eight cancer types before metastasis using Python, Keras, and TensorFlow. Improved accuracy from 70% to 83% while maintaining specificity above 99%.
RStudio Cheat Sheets
Machine learning framework for predicting the responses of drug combinations in pre-clinical studies, such as those based on cell lines or patient-derived cells.
R package to work with ctDNA sequencing data
R-package for the detection and annotation of focal CNAs
G2P is an integrated genomic selection (GS) package for predicting phenotypes from genotypes. It includes 15 GS algorithms and 13 evaluation measurements.
Deep learning simplified by transferring prior learning using the Python deep learning ecosystem
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
microsatellite instability detection using tumor only or paired tumor-normal data
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Microsatellite instability (MSI) detection for tumor only data.
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect.
ASU Research Computing :: materials from hosted workshops
Wrapper functions that make plotting in R a lot easier for beginners.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.