loopCounts: Merged loop calls with contact frequency from replicate Hi-C...
In EricSDavis/hictoolsr: An R Package for Hi-C Data Analysis
loopCounts R Documentation
Merged loop calls with contact frequency from replicate Hi-C experiments
Description
Using data from "Phase separation drives aberrant chromatin looping and
cancer development" by Ahn et al. 2021 (GEO links GSE143465 and GSE143465),
looping interactions were called with SIP (https://github.com/PouletAxel/SIP).
Resulting loop calls were merged using functions from 'hictoolsr' and
interactions were extracted from replicate '.hic' files. The resulting file
can be used to demonstrate differential loop calling between two biological
conditions.
Usage
data("loopCounts")
Format
a GInteractions object with metadata columns describing
loop properties and interaction counts from replicate
Hi-C data
References
Ahn, Jeong Hyun, Eric S. Davis, Timothy A. Daugird,
Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li,
et al. 2021. “Phase Separation Drives Aberrant Chromatin
Looping and Cancer Development.” Nature 595 (7868): 591–95.
SIP (https://github.com/PouletAxel/SIP)
EricSDavis/hictoolsr documentation built on Sept. 4, 2022, 12:36 a.m.
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| loopCounts | R Documentation |
Merged loop calls with contact frequency from replicate Hi-C experiments
Description
Using data from "Phase separation drives aberrant chromatin looping and cancer development" by Ahn et al. 2021 (GEO links GSE143465 and GSE143465), looping interactions were called with SIP (https://github.com/PouletAxel/SIP). Resulting loop calls were merged using functions from 'hictoolsr' and interactions were extracted from replicate '.hic' files. The resulting file can be used to demonstrate differential loop calling between two biological conditions.
Usage
data("loopCounts")
Format
a GInteractions object with metadata columns describing loop properties and interaction counts from replicate Hi-C data
References
Ahn, Jeong Hyun, Eric S. Davis, Timothy A. Daugird, Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li, et al. 2021. “Phase Separation Drives Aberrant Chromatin Looping and Cancer Development.” Nature 595 (7868): 591–95.
SIP (https://github.com/PouletAxel/SIP)
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.
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