PARma statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

PARma specifications

Information


Unique identifier OMICS_05258
Name PARma
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PARma

PARma in publications

 (2)
PMCID: 4437211
PMID: 26042150
DOI: 10.3389/fgene.2015.00188

[…] with growing amount of new applications of sequencing (such as clip-seq and par-clip), we anticipate that the need for comparing read profiles would increase. indeed, two recent methods (parma and paralyzer) utilized the patterns obtained after mapping short reads from par-clip to determine the mirna target sites (corcoran et al., ; erhard et al., ). here, par-clip is used […]

PMCID: 4477666
PMID: 25958398
DOI: 10.1093/nar/gkv439

[…] (i) only a small fraction of rbp binding sites are close to or on top of splice junctions or (ii) current aligners are not very efficient in mapping reads across splice junctions. clipz () and parma () are able to internally handle clip clusters that span junctions, while other pipelines such as dclip () must be fed externally with mapping data on both the genome and transcriptome in order […]


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