GenomeJack statistics

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Citations per year

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

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

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Protocols

GenomeJack specifications

Information


Unique identifier OMICS_02143
Name GenomeJack
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline GenomeJack

GenomeJack citations

 (9)
library_books

AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica

2018
PLoS Pathog
PMCID: 5884625
PMID: 29554130
DOI: 10.1371/journal.ppat.1006882

[…] e calculated by bedtools (v. 2.17.0) [] and normalized by reads per kilobase of exon per million mapped reads (RPKM) according to the method by Weedall et al []. The mapping data were visualized with GenomeJack viewer software (v 3.1) (Mitsubishi Space Software, Tokyo, Japan) (http://genomejack.net/english/index.html). The predicted gene copy number was calculated at RPKM score of each gene divide […]

call_split

Novel endogenous simian retroviral integrations in Vero cells: implications for quality control of a human vaccine cell substrate

2018
Sci Rep
PMCID: 5766633
PMID: 29330501
DOI: 10.1038/s41598-017-18934-2
call_split See protocol

[…] sensus SERV sequence found in the genome of Vero 0111 cells (GenBank: AB935214) was performed using BWA bwa-mem with the Illumina short reads of Long-PCR fragments, followed by visualization with the GenomeJack viewer software (Mitsubishi Space Software, Tokyo, Japan). […]

library_books

Myotonic dystrophy type 1 patient derived iPSCs for the investigation of CTG repeat instability

2017
Sci Rep
PMCID: 5304155
PMID: 28211918
DOI: 10.1038/srep42522

[…] are on chromosome 19 (ch19):46273584-46273607 (CTCF_1) and ch19:46273339-46273360 (CTCF_2). Finally, we performed a quantitative assessment using MAnorm. All the above results are shown in using the GenomeJack Browser (Mitsubishi Space Software Corporation, Tokyo, Japan). […]

library_books

A Comprehensive Profile of ChIP Seq Based Olig2 Target Genes in Motor Neuron Progenitor Cells Suggests the Possible Involvement of Olig2 in the Pathogenesis of Amyotrophic Lateral Sclerosis

2015
PMCID: 4437538
PMID: 26023283
DOI: 10.4137/JCNSD.S23210

[…] if sequences surrounding the peaks by using the GADEM program and the genomic location of binding peaks by a peak-finding tool of Strand NGS. We imported the processed data into a genome viewer named GenomeJack v1.4 (Mitsubishi Space Software). For RNA-Seq analysis, after removing poly-A tails and low-quality reads from NGS short-read data, we mapped them on mm9 or hg19 by TopHat version 2.0.9 (cc […]

library_books

A Comprehensive Profile of ChIP Seq Based PU.1/Spi1 Target Genes in Microglia

2014
PMCID: 4262374
PMID: 25574134
DOI: 10.4137/GRSB.S19711

[…] ding tool of Strand NGS that classifies the locations into the upstream region, 5′ untranslated region (5′UTR), exon, intron, and 3′UTR. We also imported the processed data into a genome viewer named GenomeJack v1.4 (Mit-subishi Space Software). We identified the consensus motif sequences in the genomic regions surrounding the peaks by using the GADEM program. […]

call_split

The V Protein of Canine Distemper Virus Is Required for Virus Replication in Human Epithelial Cells

2013
PLoS One
PMCID: 3866114
PMID: 24358174
DOI: 10.1371/journal.pone.0082343
call_split See protocol

[…] ed on the RNAseq analysis, the obtained short reads were mapped to the corresponding reference CDV genome sequence (007Lm-VDS) by the BWA mapping tool . The obtained mapping data were visualized with GenomeJack viewer software (Mitsubishi Space Software, Tokyo, Japan). […]


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GenomeJack institution(s)
Mitsubishi Space Software Company Limited, Tokyo, Japan

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