S3V2_IDEAS_ESMP: a package for normalizing, denoising and integrating epigenomic datasets across different cell types
The S3V2-IDEAS package first normalizes average read counts by S3V2 and then uses IDEAS to either do genome segmentations or call master peaks list across multiple datasets. This package uses bigWig files as the inputs.
Figure 1. The overview of S3V2-IDEAS package. There are two main steps in the S3V2-IDEAS package: (A) the data normalization and denoising step by S3V2 and (B and C) the data integration step by IDEAS. The data integration step has two modes. (B) In the epi-genetic state mode, multiple epigenetic features can be integrated into the epigenetic states model (D). (C) In the signal intensity state mode, the signal of one epigenetic feature can be clustered into different signal intensity states (E). (F) An additional master peak list can be extracted from the signal intensity state tracks in multiple cell types.
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(1) Prerequisites and S3V2_IDEAS_ESMP Installation
(2) Inputs-ParameterSettings-RunningSteps-Outputs for S3V2_IDEAS_ESMP
(3) Running S3V2-IDEAS in operating system set in Docker
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Guanjue Xiang, Belinda M Giardine, Shaun Mahony, Yu Zhang, Ross C Hardison, S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types, Bioinformatics, 2021;, btab148, https://doi.org/10.1093/bioinformatics/btab148
Yu Zhang, Lin An, Feng Yue, Ross C Hardison, Jointly characterizing epigenetic dynamics across multiple human cell types, Nucleic Acids Research, Volume 44, Issue 14, 19 August 2016, Pages 6721–6731, https://doi.org/10.1093/nar/gkw278
Yu Zhang, Shaun Mahony. Direct prediction of regulatory elements from partial data without imputation. PLoS computational biology. 2019 Nov 4;15(11):e1007399, https://doi.org/10.1371/journal.pcbi.1007399
Guanjue Xiang, Cheryl A Keller, Belinda Giardine, Lin An, Qunhua Li, Yu Zhang, Ross C Hardison, S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data, Nucleic Acids Research, Volume 48, Issue 8, 07 May 2020, Page e43, https://doi.org/10.1093/nar/gkaa105
a. IDEAS genome segmentation analysis for VISION project (http://usevision.org/): IDEAS Updates and the corresponding genome segmentation analysis with 8 epigenetic features in 20 mouse hematopoietic cell types.
Guanjue, Xiang, Cheryl A. Keller, ..., Yu Zhang, Ross C. Hardison. "An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis." Genome research. 2020 Mar 1;30(3):472-84, https://doi.org/10.1101/gr.255760.119
The Genome segmentation tracks is in the "IDEAS..." tab: https://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks?db=mm10
Yu Zhang, Ross C Hardison. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Nucleic acids research. 2017 Sep 29;45(17):9823-36, https://doi.org/10.1093/nar/gkx659
Genome segmentation tracks: http://bx.psu.edu/~yuzhang/Roadmap_ideas/