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Update and expansion of the website "nucleotide sequence analysis (with R)"

Research Project

Project/Area Number 18K11521
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionThe University of Tokyo

Principal Investigator

KADOTA Koji  東京大学, 大学院情報学環・学際情報学府, 准教授 (60392221)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2020: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
KeywordsR / 研究倫理 / 発現変動解析 / RNA-seq / 発現解析 / データ正規化 / Rパッケージ / パッケージ / ウェブサーバ / 文献調査 / ガイドライン / カウントデータ / バイオインフォマティクス / 統計解析
Outline of Final Research Achievements

The website "nucleotide sequence analysis (with R)" is a comprehensive information site for efficient analysis of nucleotide sequence data and gene expression data using R, an data analysis environment. The purpose is to (1) update and (2) expand the information on this website.
During the term, we not only updated basic matters such as installation procedures and basic usage, but also updated and added analysis examples. We also summarized the importance of critical reading of academic papers.

Academic Significance and Societal Importance of the Research Achievements

本ウェブサイトの情報更新・拡充を通じて、実験系研究者自身によるデータ解析を助け、日本全体の研究力向上に貢献できたと考えている。また、「なぜ次から次へと新規手法が開発されるのか?」という問いに対する明快な解答とともに、ただ論文を出せばよいわけではないという研究者としてのあるべき姿(研究倫理)を後進に示すことができた。

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (14 results)

All 2021 2020 2019 Other

All Journal Article (7 results) (of which Open Access: 7 results,  Peer Reviewed: 3 results) Presentation (1 results) (of which Invited: 1 results) Book (1 results) Remarks (5 results)

  • [Journal Article] 次世代シーケンサーデータの解析手法(第16回)なぜ次から次へと新規手法が開発されるのか?2021

    • Author(s)
      門田幸二, 清水謙多郎
    • Journal Title

      日本乳酸菌学会誌

      Volume: 32 Pages: 123-128

    • NAID

      40022749841

    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Journal Article] Methods for analyzing next-generation sequencing data XV. RNA-seq analysis (Part 3)2020

    • Author(s)
      寺田 朋子, 清水 謙多郎, 門田 幸二
    • Journal Title

      Japanese Journal of Lactic Acid Bacteria

      Volume: 31 Issue: 1 Pages: 25-34

    • DOI

      10.4109/jslab.31.25

    • NAID

      130008022525

    • ISSN
      1343-327X, 2186-5833
    • Year and Date
      2020-03-09
    • Related Report
      2020 Research-status Report
    • Open Access
  • [Journal Article] Commentary: A systematic evaluation of single cell RNA-seq analysis pipelines.2020

    • Author(s)
      Kadota K and Shimizu K
    • Journal Title

      Frontiers in Genetics

      Volume: 11 Pages: 941-941

    • DOI

      10.3389/fgene.2020.00941

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data.2019

    • Author(s)
      Osabe T, Shimizu K, Kadota K
    • Journal Title

      Bioinform Biol Insights

      Volume: 13

    • DOI

      10.1177/1177932219860817

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 次世代シーケンサーデータの解析手法:第14回RNA-seq 解析(その2)2019

    • Author(s)
      寺田朋子, 清水謙多郎, 門田幸二
    • Journal Title

      日本乳酸菌学会誌

      Volume: 30 Pages: 153-161

    • NAID

      130007928708

    • Related Report
      2019 Research-status Report
    • Open Access
  • [Journal Article] TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data2019

    • Author(s)
      Su Wei、Sun Jianqiang、Shimizu Kentaro、Kadota Koji
    • Journal Title

      BMC Research Notes

      Volume: 12 Issue: 1 Pages: 133-133

    • DOI

      10.1186/s13104-019-4179-2

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 次世代シーケンサーデータの解析手法:第13回RNA-seq 解析(その1)2019

    • Author(s)
      寺田朋子, 坂本光央, 清水謙多郎, 門田幸二
    • Journal Title

      日本乳酸菌学会誌

      Volume: 30 Pages: 38-45

    • NAID

      130007844549

    • Related Report
      2018 Research-status Report
    • Open Access
  • [Presentation] トランスクリプトーム解析分野のバイオインフォマティクス系研究者の雑感2020

    • Author(s)
      門田幸二
    • Organizer
      数理生物学セミナー2020@TMDU
    • Related Report
      2020 Research-status Report
    • Invited
  • [Book] RNA-Seqデータ解析 WETラボのための鉄板レシピ(坊農秀雅 編)2019

    • Author(s)
      門田幸二
    • Total Pages
      255
    • Publisher
      羊土社
    • ISBN
      9784758122436
    • Related Report
      2019 Research-status Report
  • [Remarks] (Rで)塩基配列解析

    • URL

      https://www.iu.a.u-tokyo.ac.jp/kadota/r_seq.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] (Rで)塩基配列解析のサブ

    • URL

      https://www.iu.a.u-tokyo.ac.jp/kadota/r_seq2.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] (Rで)塩基配列解析

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html

    • Related Report
      2020 Research-status Report 2019 Research-status Report 2018 Research-status Report
  • [Remarks] (Rで)塩基配列解析のサブ

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq2.html

    • Related Report
      2019 Research-status Report 2018 Research-status Report
  • [Remarks] TCC-GUI

    • URL

      https://github.com/swsoyee/TCC-GUI

    • Related Report
      2018 Research-status Report

URL: 

Published: 2018-04-23   Modified: 2023-01-30  

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