ChromImpute specifications


Unique identifier OMICS_11185
Name ChromImpute
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes



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  • person_outline Jason Ernst <>

Publication for ChromImpute

ChromImpute in publications

PMCID: 5715040
PMID: 29051481
DOI: 10.1038/s41467-017-01188-x

[…] different partitions were similar. the conclusions remained qualitatively the same when spearman’s rank correlation was used instead of pearson’s correlation (“methods”; supplementary figs.  and )., chromimpute is a method for imputing one functional genomic data type using multiple other data types. we compared dh predictions by bird using only gene expression data with dh predictions […]

PMCID: 5546707
PMID: 28742084
DOI: 10.1371/journal.pgen.1006933

[…] each epigenetic mark (h3k4me1, h3k4me3, h3k36me3, h3k27me3, h3k9me3, h3k27ac, h3k9ac, and dnase i hypersensitivity) in each roadmap consolidated epigenome where available. peak calls imputed using chromimpute [] were used in place of missing data. next, peak files were reduced to a per-nucleotide binary encoding of presence or absence of contiguous regions of strong chip-seq signal enrichment […]

PMCID: 5870713
PMID: 28881977
DOI: 10.1093/bioinformatics/btx243

[…] to the existing literature on structured signal recovery, in particular supervised denoising in images (; ; ) and speech (). it complements other efforts to impute missing genomic data, such as chromimpute (), which predict profiles for a missing target mark in a target cell type (e.g. h3k4me3 in embryonic stem cells) by leveraging other available marks in the target cell type (e.g. h3k27ac […]

PMCID: 5385569
PMID: 28387224
DOI: 10.1038/ncomms15011

[…] can even be applied to analyse a single mark. here the domain-level states can be used to identify broad regions occupied by the mark (). if a few marks are not measured for a cell type of interest, chromimpute can be used to impute the missing data before applying dihmm. finally, while we have only focused on a two-level model implementation in this paper, it can be naturally extended […]

PMCID: 4931220
PMID: 27346250
DOI: 10.1038/ncomms11306

[…] recover lost dmps by imputation which proved highly successful for the recovery of single nucleotide polymorphisms (snps) in low-coverage whole-genome sequencing. towards this goal, a first method (chromimpute) was recently developed and shown to be capable of imputing epigenomic maps with as little as 26% of supporting experimental data. while the imputed data were similar to the observed […]

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ChromImpute institution(s)
Department of Biological Chemistry, University of California, Los Angeles, CA, USA; Computer Science Department, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA

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