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adage

This is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)

akutils-v1.2

akutils with massive updates over v1.1 to functionality and command line interface.

ampliconarchitect

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.

applied-deep-learning-with-keras

Deep Learning examples with Keras.

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bioinfo

Bioinformatics tools

bmc

Notes on Scientific Computing for Biomechanics and Motor Control

brain2020

Development and validation of an interpretable deep learning framework for Alzheimer's disease classification

cancerlocator

A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.

cancerseekv1

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.

cdnn

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%.

cheatsheets

RStudio Cheat Sheets

cnaclinic

combofm

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.

ctdnatools

R package to work with ctDNA sequencing data

delfi_scripts

demultiplexing

earlycancerdetection

focalcall

R-package for the detection and annotation of focal CNAs

g2p

G2P is an integrated genomic selection (GS) package for predicting phenotypes from genotypes. It includes 15 GS algorithms and 13 evaluation measurements.

hands-on-transfer-learning-with-python

Deep learning simplified by transferring prior learning using the Python deep learning ecosystem

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

integral-anc-curve-fitting

ml

msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

prepareaa

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect.

rcworkshops

ASU Research Computing :: materials from hosted workshops

rplotter

Wrapper functions that make plotting in R a lot easier for beginners.