piClust protocols

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piClust specifications

Information


Unique identifier OMICS_07341
Name piClust
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Inuk Jung <>

Publication for piClust

piClust in pipeline

2018
PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] genome reference produced by repeatmasker () as described previously in color space using bowtie, reporting at maximum five valid alignments. finally, our sorted alignment files were submitted to piclust software (). here, the eps parameter was set to 1000 and minreads to 50., total dna from a single a. viridis polyp (normal seawater conditions, ph 8.2) was extracted and subjected to whole […]


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piClust in publications

 (5)
PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] genome reference produced by repeatmasker () as described previously in color space using bowtie, reporting at maximum five valid alignments. finally, our sorted alignment files were submitted to piclust software (). here, the eps parameter was set to 1000 and minreads to 50., total dna from a single a. viridis polyp (normal seawater conditions, ph 8.2) was extracted and subjected to whole […]

PMCID: 5751586
PMID: 29297285
DOI: 10.1186/s12859-017-1896-1

[…] approaches based on clustering locus of pirnas, protrac [] can identify pirna clusters and pirnas from a small rna-seq dataset through a probabilistic analysis of mapped sequence reads. furthermore, piclust [] uses a density-based clustering method to identify pirna clusters without assuming any parametric distribution model. besides, the sequence-based approach can further incorporate […]

PMCID: 5452642
PMID: 28472327
DOI: 10.1093/gbe/evx087

[…] smallest sequence in the genome assembly v4.5 is around 800 bp) and containing at least four different pirnas were considered as a pirna cluster candidate. in a second approach, we used the software piclust to predict pirna cluster candidates () with a 5-kb sliding window, with at least five reads per cluster and a cutscore parameter of 3. only clusters predicted by both methods are reported., […]

PMCID: 5260113
PMID: 28155667
DOI: 10.1186/s12918-016-0355-3

[…] regions, referred to as phasirnas []. we also found that many genes harbor sirna dense clusters within their gene body using a modified version of our previously implemented density based algorithm, piclust []. this clustering algorithm was used to eliminate noise in the data and efficiently detect highly reliable sirna enriched clusters. piclust is based on the well known dbscan algorithm [], […]

PMCID: 4869193
PMID: 27183847
DOI: 10.1186/s12864-016-2697-z

[…] patterns in germline cells, different melanoma types and healthy skin., prior to developing our own pirna clustering pipeline we tested two already publicly available tools, protrac [] and piclust []. we excluded piclust, because of the restriction to selected genomes, file size and the limited number of multiple mapping sites per read. using our dataset protrac resulted […]


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piClust institution(s)
Interdisciplinary Program in Bioinformatics, Korea

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