metamaden

recountmethylation

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

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.

lute

R package for deconvolution simulation and optimization.

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.

awesome-deconvolution

List of deconvolution methods and resources.

metamaden.github.io

Professional resume, portfolio, bio, and presentations for Sean K. Maden, Ph.D.

NextFlow-Workshop

NextFlow workshop materials for LIBD Rstats club presentation.

r-nf_deconvolution

Deconvolution NextFlow workflow using R and Rscripts.

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.

edirect_docker

Make the Entrez Direct Utilites Docker image

nextflow_examples

Example NextFlow workflows using R scripts for benchmarking tasks.

recountmethylation_bioc2021

Learning materials, including presentation slides and code, cheat sheet, and wiki, for the recountmethylation Bioc2021 software demo.

awesome-nextflow-benchmark

List of NextFlow workflows for benchmarking.

bisque

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

BrainCellularComposition

bseqsc

Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline

cellScaleFactors

R/Bioconductor datasets compiling cell scale factor references for deconvolution.

code_portfolio

Professional portfolio of code and code applications.

deconrnaseqParam

Object class definition and methods for deconrnaseqParam, a type of deconvolution algorithm.

epicParam

Object class definition and methods for EPIC, a type of deconvolution algorithm.

GEM

meanratiosParam

Object class for mean ratios, a type of marker selection strategy.

MuSiC

Multi-subject Single Cell Deconvolution

music2Param

Object class definition and methods for MuSiC2, a type of deconvolution algorithm.

musicParam

Object class definition and methods for MuSiC, a type of deconvolution algorithm.

recountmethylation_flexible-blood-analysis_manuscript

Supplemental materials for the recountmethylation v2 manuscript

sean_maden_biosketch_versions

Biosketch for Sean Maden

Svelvet

A lightweight Svelte component library for building interactive node-based flow diagrams

Tutorial-Sim_Cluster_Composer

A tutorial on automating R simulation studies with clusters