DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity.
DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity.
复制标题
DOI：
10.1093/bioinformatics/btad039
复制
发表时间：
2023-01-01
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
基因表达的昼夜节律振荡调节日常生理过程，其中断与许多疾病有关。昼夜节律可以以各种方式被破坏，包括差分相位、幅度和节律适应性。尽管已经提出了许多差异性昼夜节律生物标志物检测方法，但是目前还没有一种具有准确假阳性对照的多方面差异性昼夜节律特征的系统检测的工作流程。我们提出了一个全面的和互动的管道，以捕捉差异节律生物标志物的多方面特征。分析输出伴随着信息可视化和交互式探索。该工作流程在多个案例研究中得到了证明，并可扩展到一般的组学应用程序。R包、Shiny应用程序和源代码可在GitHub（https：//github.com/DiffCircaPipeline）和Zenodo（https：//doi.org/10.5281/zenodo.7507989）中获得。补充数据可在Bioinformatics在线获得。
Circadian oscillations of gene expression regulate daily physiological processes, and their disruption is linked to many diseases. Circadian rhythms can be disrupted in a variety of ways, including differential phase, amplitude and rhythm fitness. Although many differential circadian biomarker detection methods have been proposed, a workflow for systematic detection of multifaceted differential circadian characteristics with accurate false positive control is not currently available. We propose a comprehensive and interactive pipeline to capture the multifaceted characteristics of differentially rhythmic biomarkers. Analysis outputs are accompanied by informative visualization and interactive exploration. The workflow is demonstrated in multiple case studies and is extensible to general omics applications. R package, Shiny app and source code are available in GitHub (https://github.com/DiffCircaPipeline) and Zenodo (https://doi.org/10.5281/zenodo.7507989) Supplementary data are available at Bioinformatics online.
登录
查看更多内容
影响因子：
5.8
作者：
Thaben, Paul F.;Westermark, Pal O.
通讯作者：
Westermark, Pal O.
DOI：
10.1073/pnas.1508249112
发表时间：
2016-01-05
影响因子：
11.1
作者：
Chen, Cho-Yi;Logan, Ryan W.;McClung, Colleen A.
通讯作者：
McClung, Colleen A.
影响因子：
5.8
作者：
Parsons, Rex;Parsons, Richard;Rawashdeh, Oliver
通讯作者：
Rawashdeh, Oliver
影响因子：
3.5
作者：
Hughes ME;Abruzzi KC;Allada R;Anafi R;Arpat AB;Asher G;Baldi P;de Bekker C;Bell-Pedersen D;Blau J;Brown S;Ceriani MF;Chen Z;Chiu JC;Cox J;Crowell AM;DeBruyne JP;Dijk DJ;DiTacchio L;Doyle FJ;Duffield GE;Dunlap JC;Eckel-Mahan K;Esser KA;FitzGerald GA;Forger DB;Francey LJ;Fu YH;Gachon F;Gatfield D;de Goede P;Golden SS;Green C;Harer J;Harmer S;Haspel J;Hastings MH;Herzel H;Herzog ED;Hoffmann C;Hong C;Hughey JJ;Hurley JM;de la Iglesia HO;Johnson C;Kay SA;Koike N;Kornacker K;Kramer A;Lamia K;Leise T;Lewis SA;Li J;Li X;Liu AC;Loros JJ;Martino TA;Menet JS;Merrow M;Millar AJ;Mockler T;Naef F;Nagoshi E;Nitabach MN;Olmedo M;Nusinow DA;Ptáček LJ;Rand D;Reddy AB;Robles MS;Roenneberg T;Rosbash M;Ruben MD;Rund SSC;Sancar A;Sassone-Corsi P;Sehgal A;Sherrill-Mix S;Skene DJ;Storch KF;Takahashi JS;Ueda HR;Wang H;Weitz C;Westermark PO;Wijnen H;Xu Y;Wu G;Yoo SH;Young M;Zhang EE;Zielinski T;Hogenesch JB
通讯作者：
Hogenesch JB
DOI：
10.1111/rssb.12122
发表时间：
2016-03-01
影响因子：
5.8
作者：
G'Sell, Max Grazier;Wager, Stefan;Tibshirani, Robert
通讯作者：
Tibshirani, Robert