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RIKEN::Laboratory for Medical Science Mathematics

PhD (Medicine) and Ph.D (Engineering). Group Director, Chief Scientist. Medical Science Mathematics,. RIKEN Center for Integrative Medical Sciences. 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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RIKEN::Laboratory for Medical Science Mathematics | emu.src.riken.jp Reviews
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PhD (Medicine) and Ph.D (Engineering). Group Director, Chief Scientist. Medical Science Mathematics,. RIKEN Center for Integrative Medical Sciences. 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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KEYWORDS
1 tatsuhiko tsunoda
2 members
3 publications
4 tools
5 cnvphaserpro
6 cnvphaser
7 mocsphaser
8 motifcombinator
9 cisnetview
10 hzanalyzer
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tatsuhiko tsunoda,members,publications,tools,cnvphaserpro,cnvphaser,mocsphaser,motifcombinator,cisnetview,hzanalyzer,parahaplo,exrat,ngs analyzer,vcmm,tfbind,arete,siml,address
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RIKEN::Laboratory for Medical Science Mathematics | emu.src.riken.jp Reviews

https://emu.src.riken.jp

PhD (Medicine) and Ph.D (Engineering). Group Director, Chief Scientist. Medical Science Mathematics,. RIKEN Center for Integrative Medical Sciences. 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

INTERNAL PAGES

emu.src.riken.jp emu.src.riken.jp
1

Arete - network-based gene prioritisation toolkit

http://emu.src.riken.jp/arete/arete.html

Arete - an analysis toolkit for network-based gene prioritisation. 3) Algorithms and examples. 31) Random walk with restart algorithm. 33) Arete - integrative analysis example. 5) Appendix I - downloads and example files index. Website updated on 09/12/2016. The Arete application is packaged as a plug-in app for the Cytoscape suite v3.3.0. To deploy Cytoscape, please follow the instructions at www.cytoscape.org. To install Arete App, download the compiled cy arete-2.1.jar. 3) Algorithms and examples.

2

MCV: MUTATON CALLING with VAF for WHOLE GENOME SEQUENCING

http://emu.src.riken.jp/MCV

MCV : MUTATON CALLING with VAF for WHOLE GENOME SEQUENCING. Pipeline to identify somatic substitutions and indels with VAF (variant allele frequency) from whole genome sequencing. MCV (download zip file). Two input files and one program are additionally required. BAM file after removal of PCR duplication (sorted by location). File containing mean, standard deviation of library (see example.stat). Process outline for mutation calling. 1-1) Build addXFtag and getSet123. 1-2) Add tags to bam file. AddXFtag ...

3

RIKEN::Laboratory for Medical Science Mathematics

http://emu.src.riken.jp/hzAnalyzer

R and Java for Detection and Analysis of. Contiguous Homozygosity in High-density Genotyping Datasets. To get started, you will need to have installed a relatively recent version of R. We recommend at least the latest version, which is currently R 3.0.1. Binary installation packages are available from the R project website. Additionally, hzAnalyzer makes use of Java as well as the R packages roxygen, rJava, parallel (on Unix/Linux/Mac OS X), and cluster. You will also need to install Bioconductor. A desc...

4

ExRAT

http://emu.src.riken.jp/k_softwares

ParaHaplo, ExRAT, and NGS analyzer. Software tools for k and other computers. Tools for haplotype-based whole-genome association study using parallel computing. Open source code for k and other computers. Developed by Kazuharu Misawa. Download tar gz file). Tools for association study with interaction. Open source code for k and other computers. Developed by Eiji Nakamura, Reiichiro Nakamichi, Takashi Morizono, and Tatsuhiko Tsunoda. Download tar gz file). Open source code for k computer.

5

HML: Tool to perform Hierarchical Maximum Likelihood (HML) Clustering

http://emu.src.riken.jp/HML

HML : Tool to perform Hierarchical Maximum Likelihood (HML) Clustering. HML (download tar file). Codes are written in Matlab. The following codes are provided:. Run this code to test HML clustering approach. Run to perform HML clustering. Function used by HML.m. Ref: A. Sharma et al., Hierarchical maximum likelihood clustering approach, IEEE Transactions on Bio-Medical Engineering, 2016.

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ims.riken.jp ims.riken.jp

研究室紹介 | 理化学研究所 統合生命医科学研究センター(IMS)

http://www.ims.riken.jp/laboratories

個別化医療 個別化予防の実現に向けて、ヒトのゲノムを解析する基盤を構築するとともに、がん 循環器疾患 糖尿病等の疾患の発症 予後や、薬剤反応性に関わる遺伝 環境要因を網羅的に解析し、医療への応用のための技術開発研究を行います。 YOUNG CHIEF INVESTIGATORS 詳しくはこちら.

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RIKEN::Laboratory for Medical Science Mathematics

PhD (Medicine) and Ph.D (Engineering). Group Director, Chief Scientist. Medical Science Mathematics,. RIKEN Center for Integrative Medical Sciences. 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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