metamaden
Postdoc with Hicks Lab at JHU Biostatistics (remote); Topics: brain, single-cell RNAseq, deconvolution, machine learning, epigenetics; Tools: R, Python, bash.
Department of Biostatistics, JHSPHremote
Pinned Repositories
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's Repositories
metamaden/recountmethylation
Utilities to access and analyze harmonized databases of public DNAm arrays from GEO.
metamaden/cgmappeR
Map and visualize genomic CpGs (shinyR)
metamaden/geoarraydigest
Resource for summarizing and tracking new array samples published to NCBI's Gene Expression Omnibus (GEO) database.
metamaden/lute
R package for deconvolution simulation and optimization.
metamaden/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.
metamaden/awesome-deconvolution
List of deconvolution methods and resources.
metamaden/cellScaleFactors
R/Bioconductor datasets compiling cell scale factor references for deconvolution.
metamaden/metamaden.github.io
Professional resume, portfolio, bio, and presentations for Sean K. Maden, Ph.D.
metamaden/NextFlow-Workshop
NextFlow workshop materials for LIBD Rstats club presentation.
metamaden/r-nf_deconvolution
Deconvolution NextFlow workflow using R and Rscripts.
metamaden/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/edirect_docker
Make the Entrez Direct Utilites Docker image
metamaden/nextflow_examples
Example NextFlow workflows using R scripts for benchmarking tasks.
metamaden/recountmethylation_bioc2021
Learning materials, including presentation slides and code, cheat sheet, and wiki, for the recountmethylation Bioc2021 software demo.
metamaden/awesome-nextflow-benchmark
List of NextFlow workflows for benchmarking.
metamaden/BrainCellularComposition
metamaden/bseqsc
Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
metamaden/code_portfolio
Professional portfolio of code and code applications.
metamaden/deconrnaseqParam
Object class definition and methods for deconrnaseqParam, a type of deconvolution algorithm.
metamaden/epicParam
Object class definition and methods for EPIC, a type of deconvolution algorithm.
metamaden/GEM
metamaden/gh-website
Host a professional or personal website on GitHub.
metamaden/meanratiosParam
Object class for mean ratios, a type of marker selection strategy.
metamaden/MuSiC
Multi-subject Single Cell Deconvolution
metamaden/music2Param
Object class definition and methods for MuSiC2, a type of deconvolution algorithm.
metamaden/musicParam
Object class definition and methods for MuSiC, a type of deconvolution algorithm.
metamaden/recountmethylation_flexible-blood-analysis_manuscript
Supplemental materials for the recountmethylation v2 manuscript
metamaden/sean_maden_biosketch_versions
Biosketch for Sean Maden
metamaden/Svelvet
A lightweight Svelte component library for building interactive node-based flow diagrams
metamaden/Tutorial-Sim_Cluster_Composer
A tutorial on automating R simulation studies with clusters