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Paraclu specifications

Information


Unique identifier OMICS_21177
Name Paraclu
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 9.0
Stability Stable
Requirements
a C++ compiler.
Source code URL http://people.binf.ku.dk/albin/supplementary_data/tss_code/
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Martin Frith
  • person_outline Albin Sandelin
  • person_outline Paraclu Team

Additional information


http://cbrc3.cbrc.jp/~martin/paraclu/README.txt

Publication for Paraclu

Paraclu citations

 (8)
library_books

A genome wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve

2018
BMC Genomics
PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] eads generated per library). The sequencing data was analyzed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), filtered using TagDust2 [], mapped using BWA [], clustered using Paraclu [], and visualized using BEDtools [] and the UCSC Genome Browser []. […]

library_books

The effect of genetic variation on promoter usage and enhancer activity

2017
Nat Commun
PMCID: 5677018
PMID: 29116076
DOI: 10.1038/s41467-017-01467-7

[…] http://fantom.gsc.riken.jp/5/data/). Enhancer elements characterized with bidirectional transcription patterns in our samples were selected. To this end, we first produced CAGE tag clusters using the Paraclu method (V9), with CAGE tag 5′ genomic coordinates as input and (i) a minimum of five tags per cluster, (ii) a (maximum density)/(baseline density) ≥ 2 and (iii) a maximal cluster length of 200 […]

library_books

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth

2017
Sci Rep
PMCID: 5597620
PMID: 28904364
DOI: 10.1038/s41598-017-11574-6

[…] tained. Gencode v19, was used to annotate the TC, resulting in 14,018 annotated genes. Expression values for these TCs were computed by using BedTools to intersect the unfiltered CTSS files with the Paraclu-determined TC genomic boundaries. […]

library_books

Single Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

2016
J Virol
PMCID: 5110153
PMID: 27681123
DOI: 10.1128/JVI.01625-16

[…] preS/S is as high as pgRNA in the mouse AAV-HBV model, whereas the expression of pgRNA is predominant in the other models (). We then independently performed peak calling for the model systems using Paraclu with the same parameters used for the clinical samples. We identified 15 peaks, 10 of which overlap the clinical peaks (5 of 6 major peaks and 5 of 11 minor peaks), indicating that a majority […]

library_books

Global transcript structure resolution of high gene density genomes through multi platform data integration

2016
Nucleic Acids Res
PMCID: 5062983
PMID: 27407110
DOI: 10.1093/nar/gkw629

[…] q's utilization of SMART (Switching Mechanism At 5′ end of RNA Template) cDNA synthesis ()) would make deepCAGE well suited for testing the veracity of CFL 5′ ends. DeepCAGE tags were clustered using Paraclu () and putative transcription start sites were calculated as the average chromosomal start coordinate weighted by CAGE tag depth. Iso-Seq 5′ end clusters were identified as described in the ‘M […]

library_books

Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera

2015
Sci Rep
PMCID: 4466890
PMID: 26073445
DOI: 10.1038/srep11136

[…] To define TSS positions, CAGE tags belonging to each sample were clustered using an iterative hierarchical clustering approach with Paraclu v9 to form clusters covering regions of less than 50 bp (). Clusters that were more than 50 bp in length or were represented by fewer than 5 tags after rescaling were removed. Clusters with a […]

Citations

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Paraclu institution(s)
Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan; ARC Centre in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; The Bioinformatics Centre, Department of Molecular Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes, Denmark; Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Saitama, Japan
Paraclu funding source(s)
Supported by a Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government; a grant of the Genome Network Project from the Ministry of Education, Culture, Sports, Science, and Technology, Japan; the Strategic Programs for R&D of RIKEN Grant for the RIKEN Frontier Research System, Functional RNA research program; and a grant from the Novo Nordisk Foundation to the Bioinformatics Centre.

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