metamaden

awesome-deconvolution

List of deconvolution methods and resources.

cgmappeR

Map and visualize genomic CpGs (shinyR)

geoarraydigest

Resource for summarizing and tracking new array samples published to NCBI's Gene Expression Omnibus (GEO) database.

hm450hg38manifest

Manifest prepared for HM450 array with hg38 genome build

lute

R package for deconvolution simulation and optimization.

methyPre

Methylation array preprocessing.

r-nf_deconvolution

Deconvolution NextFlow workflow using R and Rscripts.

recountmethylation

Utilities to access and analyze harmonized databases of public DNAm arrays from GEO.

recountmethylation.pipeline

Functions and utilities for pipeline to compile and harmonize public GEO DNA methylation array data and sample metadata. For implementation, see the `recountmethylation_instance` resource.

recountmethylation_instance

Synchronize public DNAm array data. This resource provides a full Snakemake workflow to download, harmonize, and compile IDAT-derived DNAm and SOFT-derived sample metadata from GEO experiments.

metamaden/recountmethylationManuscriptSupplement

Supplemental methods, scripts, and code for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus"

metamaden/recountmethylation_server

Server code for Recount-Methylation database.

metamaden/bisque

An R toolkit for estimation of cell composition from bulk expression data

metamaden/cmlmanuscript

Resources to reproduce analysis for the manuscript "Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk."

metamaden/consensus_machine_learning

Package to reproduce analyses for the manuscript "Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk".

metamaden/figshare-doi-badge

testing badge inclusion in readme

metamaden/google-research

Google Research

metamaden/hexSticker

:sparkles: Hexagon sticker in R

metamaden/IntegratedATACseqAnalysisWorkshop2021

metamaden/Keras-GAN

Keras implementations of Generative Adversarial Networks.

metamaden/kma

Keep Me Around: Intron Retention Detection

metamaden/lucid

A collection of infrastructure and tools for research in neural network interpretability.

metamaden/machine-learning

CS545 scripts, homework, and info for Fall quarter 2018.

metamaden/methylCC

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

metamaden/MTG_celltypes

Human cortical cell types

metamaden/neoepiscope

predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data

metamaden/neoepiscope-paper

Scripts for reproducing results from neoepiscope paper

metamaden/Net-Trim

The latest version of Net-Trim which solves the actual constrained problem

metamaden/pix2pix

Image-to-image translation with conditional adversarial nets

metamaden/recount.synth

Resources for research synthesis

metamaden/recountmethylation_hexsticker

Make the hex sticker for Recount Methylation and affiliated software.

metamaden/recountmethylation_manuscript_supplement

Supplement for the manuscript "Human methylome variation across Infinium 450K data onthe Gene Expression Omnibus"

metamaden/rienv

Retained intron environment.

metamaden/RNAseq_Cancer_Biomarkers

Machine Learning to Detect Cancer Biomarkers from RNAseq Data

metamaden/scaden

Deep Learning based cell composition analysis with Scaden.

metamaden/SpatialExperiment_Bioc2021

metamaden/tlverse-handbook

🎯 :closed_book: Targeted Learning in R: Causal Data Science with the tlverse

metamaden/txt2onto

Code for classifying unstructured text to tissue ontology terms using natural language processing and machine learning.

metamaden/UMtools

An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level

metamaden/vapoRwave

📼👾🕹Vaporwave themes and color palettes for ggplot2💾👨‍🎤📺