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/methyPre
Methylation array preprocessing.
metamaden/hm450hg38manifest
Manifest prepared for HM450 array with hg38 genome build
metamaden/galaxy-hub
Galaxy Community Hub
metamaden/geneMapR
Repo containing info and workhorse scripts to aid gene ID mapping and coordinate retrieval.
metamaden/academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
metamaden/colon_superenhancer_methylation_project
Colon super-enhancer methylation impacts gene expression in a tissue-specific manner in colorectal cancer.
metamaden/GANs_for_Credit_Card_Data
metamaden/gdc_download_tools
Directions and code for generic GDC data downloads.
metamaden/GEOracle
metamaden/glab_posters_and_presentations
Posters related to work performed by Grady Lab
metamaden/GoodDoc
A Template for Clear and Simple Documentation of Bioinformatics Code
metamaden/HCA
metamaden/InfiniumPurifyR
Estimate tumor enrichment from methylation array data.
metamaden/methyIntegratoR
R library for integrated analysis involving methylation arrays and other molecular data.
metamaden/Nicole_Gladish
Analysis Code for Published Manuscripts
metamaden/PrImiR
Database of pairwise consensuses for miR-mRNA target interactions
metamaden/PubCode
An app platform for CLI Apps that engage NCBI/NLM Data and Services
metamaden/Python_tools
Various tools using Python
metamaden/R_examples
Example scripts for miscellaneous and bioinformatics-related imaging and analysis.
metamaden/seq_answers
Sequencing data preprocessing