In aryeelab/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).
aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.