AREM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool AREM
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Tool usage distribution map

This map represents all the scientific publications referring to AREM per scientific context
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Associated diseases

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Protocols

AREM specifications

Information


Unique identifier OMICS_07424
Name AREM
Alternative name Aligning Reads by Expectation Maximization
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Xiaohui Xie

Additional information


https://github.com/jakebiesinger/AREM

Publication for Aligning Reads by Expectation Maximization

AREM citations

 (2)
library_books

The effect of Nipped B like (Nipbl) haploinsufficiency on genome wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome

2017
Clin Epigenetics
PMCID: 5574093
PMID: 28855971
DOI: 10.1186/s13148-017-0391-x

[…] tes [, , , ]. This is consistent with the close correlation of the presence of other cohesin subunits at identified Rad21-binding sites [] (Fig. b).Fig. 1 Cohesin-binding sites were identified using AREM [], with a significance cutoff based on a p value less than 1 × 10−4, resulting in a FDR below 3.0% (Fig. a). Cohesin-binding peaks ranged from ~ 200 bp to ~ 6 kb in size with the majority less t […]

call_split

Transposable elements reveal a stem cell specific class of long noncoding RNAs

2012
Genome Biol
PMCID: 3580499
PMID: 23181609
DOI: 10.1186/gb-2012-13-11-r107
call_split See protocol

[…] e choice of one alignment per read for these meta-feature analyses should mitigate multi-mapping read challenges. Second, we remapped the reads allowing up to 20 alignments and called peaks using the AREM software package, which implements an iterative algorithm to optimally allocate multi-mapping reads built on top of the MACS method [,]. […]


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AREM institution(s)
Department of Biological Chemistry, University of California, Irvine, CA, USA; Department of Computer Science, University of California, Irvine, CA, USA; The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA
AREM funding source(s)
Partly supported by the NSF (grant DBI-0846218) and the NIH (grant HD062951) and the NIH/NLM Bioinformatics (training grant T15LM07443).

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