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ben-laufer

Special repository to add a README.md to GitHub profile

ben-laufer.github.io

biocthis

Automate package and project setup for Bioconductor packages

cffdna-and-brain-manuscript

Analyses for the manuscript "Multi-omic Brain and Behavioral Correlates of Cell-free Fetal DNA Methylation in Macaque Maternal Obesity Models."

cgi

Takes output from DMRichR and performs statistical testing and visualization for CpG and genic annotation enrichments

chipseeker

:dart:ChIP peak Annotation, Comparison and Visualization

comethyl

An R package for weighted region comethylation network analysis (Under development).

cpg_me

A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)

dmrfinder

A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data

dmrichr

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

fastq_me

An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me

flowsorted.blood.wgbs.blueprint

A Bioconductor ExperimentHub data package for flow sorted purified whole blood cell types measured using DNA methylation on WGBS platform from BLUEPRINT

gg4way

Repository for the gg4way BioConductor package

gofuncr

R-package for GO-enrichment analyses

lola

Locus Overlap Analysis: Enrichment of Genomic Ranges

low-pass-wgbs-of-ds-ndbs

Analyses for the manuscript "Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles"

methylcc

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

pcb-placenta-and-brain

Analyses for the manuscript "Prenatal PCB exposure alters a shared neurodevelopmental DNA methylation profile in mouse placenta and fetal brain".

rna-seq

RNA-seq alignment and analysis pipeline

scdotplot

Repository for the scDotPlot BioConductor package

tag-seq

3’ Tag RNA-seq pipeline (Work in progress)