diffloop: Identifying differential DNA loops from chromatin topology data
In diffloop: Identifying differential DNA loops from chromatin topology data

library(diffloop)
library(diffloopdata)
library(ggplot2)
library(GenomicRanges)
library(ggrepel)
library(DESeq2)

About

Due to the maintainer's inability to figure out data package resubmission to Bioc, a compiled vignette is hosted here.

Notes on Data

All data used in these analyses were processed from GEO and are contained in the diffloopdata package. Please feel free to contact Caleb (the maintainer) with any questions concerning the data or this workflow. The diffloopdata package is available here

Session info

sessionInfo()

Citations

$^1$Hnisz, Denes, et al. "Activation of proto-oncogenes by disruption of chromosome neighborhoods." Science (2016).

$^2$Ji, Xiong, et al. "3D Chromosome Regulatory Landscape of Human Pluripotent Cells." Cell stem cell (2015).

$^3$Phanstiel, D, et al. "Mango: A bias correcting ChIA-PET analysis pipeline." Bioinformatics (2015).

$^4$Robinson, M, et al. "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data." Bioinformatics (2010).

$^5$Law, C, et al. "Voom: precision weights unlock linear model analysis tools for RNA-seq read counts." Genome Biology (2014).