| Title: | Promoter Capture Hi-C data |
|---|---|
| Description: | Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. |
| Authors: | Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov |
| Maintainer: | Mikhail Spivakov <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.40.0 |
| Built: | 2026-10-10 11:20:16 UTC |
| Source: | https://github.com/bioc/PCHiCdata |
Promoter Capture data Hi-C conveniently packaged for consumption by R users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.
| Package: | PCHiCdata |
| Type: | Package |
| Version: | 0.1 |
| Date: | 2015-05-22 |
| License: | Artistic-2.0 |
| Depends: | R (>= 3.1.2), Chicago |
| LazyData: | true |
Index:
sGM12878 Promoter Capture data for chromosomes 20 and 21
in GM12878
smESC Promoter Capture data for chromosomes 18 and 19
in smESC
Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett, Steven Wingett
Maintainer: Paula Freire-Pritchett <[email protected]>
Mifsud, B. et al. "Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C." Nature Genetics (2015) doi:10.1038/ng.3286
Schoenfelder, S. et al. "The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements." Genome research 25.4 (2015): 582-597.
data(sGM12878) data(smESC)data(sGM12878) data(smESC)
Promoter Capture data to be used as a toy example to run all steps of Chicago. This data only incorporates read pairs including both chromosomes 20 and 21 in order to minimize processing time and memory storage. Thus, this data set includes all cis read pairs for these two chromosomes and all trans read pairs between them.
The hg19 genome was used.
The package includes ChIP-seq data from the ENCODE consortium, also restricted to chr20 and chr21. (The ENCODE Project Consortium, 2012 "An Integrated Encyclopedia of DNA Elements in the Human Genome." Nature 489 (September): 57-74. Data accession numbers: Bernstein lab GSM733752, GSM733772, GSM733708, GSM733664, GSM733771, GSM733758)
sGM12878sGM12878
A ChicagoData object.
A chicagoData object.
Mifsud, B. et al. "Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C." Nature Genetics (2015) doi:10.1038/ng.3286
data(sGM12878) ##modifications to sGM12878, ensuring it uses correct design directory designDir <- file.path(system.file("extdata", package="PCHiCdata"), "hg19TestDesign") sGM12878 <- modifySettings(cd = sGM12878, designDir=designDir)data(sGM12878) ##modifications to sGM12878, ensuring it uses correct design directory designDir <- file.path(system.file("extdata", package="PCHiCdata"), "hg19TestDesign") sGM12878 <- modifySettings(cd = sGM12878, designDir=designDir)
Promoter Capture data to be used as a toy example to run all steps of Chicago. This data only incorporates read pairs including both chromosomes 18 and 19 in order to minimize processing time and memory storage. Thus, this data set includes all cis read pairs for these two chromosomes and all trans read pairs between them.
The mm9 genome was used.
The package includes ChIP-seq data from the ENCODE consortium, also restricted to chr18 and chr19. (The ENCODE Project Consortium, 2012 "An Integrated Encyclopedia of DNA Elements in the Human Genome." Nature 489 (September): 57-74. Data accession numbers: Snyder lab GSM1003750, GSM1003756, GSM1003751; Ren lab GSM1000126, Hardison lab ENCFF001ZJO, ENCFF001ZQY)
smESCsmESC
A ChicagoData object.
A chicagoData object.
Schoenfelder, S. et al. "The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements." Genome research 25.4 (2015): 582-597.
data(smESC) ##modifications to smESC, ensuring it uses correct design directory designDir <- file.path(system.file("extdata", package="PCHiCdata"), "mm9TestDesign") smESC <- modifySettings(cd = smESC, designDir=designDir)data(smESC) ##modifications to smESC, ensuring it uses correct design directory designDir <- file.path(system.file("extdata", package="PCHiCdata"), "mm9TestDesign") smESC <- modifySettings(cd = smESC, designDir=designDir)