A step-by-step guide to analyzing CAGE data using R/Bioconductor

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A step-by-step guide to analyzing CAGE data using R/Bioconductor. / Thodberg, Malte; Sandelin, Albin.

In: F1000Research, Vol. 8, 886, 18.06.2019.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Thodberg, M & Sandelin, A 2019, 'A step-by-step guide to analyzing CAGE data using R/Bioconductor', F1000Research, vol. 8, 886. https://doi.org/10.12688/f1000research.18456.1

APA

Thodberg, M., & Sandelin, A. (2019). A step-by-step guide to analyzing CAGE data using R/Bioconductor. F1000Research, 8, [886]. https://doi.org/10.12688/f1000research.18456.1

Vancouver

Thodberg M, Sandelin A. A step-by-step guide to analyzing CAGE data using R/Bioconductor. F1000Research. 2019 Jun 18;8. 886. https://doi.org/10.12688/f1000research.18456.1

Author

Thodberg, Malte ; Sandelin, Albin. / A step-by-step guide to analyzing CAGE data using R/Bioconductor. In: F1000Research. 2019 ; Vol. 8.

Bibtex

@article{cb7118f71f174edb8697a11627f189dd,
title = "A step-by-step guide to analyzing CAGE data using R/Bioconductor",
abstract = "Cap Analysis of Gene Expression (CAGE) is one of the most popular 5'-end sequencing methods. In a single experiment, CAGE can be used to locate and quantify the expression of both Transcription Start Sites (TSSs) and enhancers. This is workflow is a case study on how to use the CAGEfightR package to orchestrate analysis of CAGE data within the Bioconductor project. This workflow starts from BigWig-files and covers both basic CAGE analyses such as identifying, quantifying and annotating TSSs and enhancers, advanced analysis such as finding interacting TSS-enhancer pairs and enhancer clusters, to differential expression analysis and alternative TSS usage. R-code, discussion and references are intertwined to help provide guidelines for future CAGE studies of the same kind.",
author = "Malte Thodberg and Albin Sandelin",
year = "2019",
month = jun,
day = "18",
doi = "10.12688/f1000research.18456.1",
language = "English",
volume = "8",
journal = "F1000Research",
issn = "2046-1402",
publisher = "F1000Research",

}

RIS

TY - JOUR

T1 - A step-by-step guide to analyzing CAGE data using R/Bioconductor

AU - Thodberg, Malte

AU - Sandelin, Albin

PY - 2019/6/18

Y1 - 2019/6/18

N2 - Cap Analysis of Gene Expression (CAGE) is one of the most popular 5'-end sequencing methods. In a single experiment, CAGE can be used to locate and quantify the expression of both Transcription Start Sites (TSSs) and enhancers. This is workflow is a case study on how to use the CAGEfightR package to orchestrate analysis of CAGE data within the Bioconductor project. This workflow starts from BigWig-files and covers both basic CAGE analyses such as identifying, quantifying and annotating TSSs and enhancers, advanced analysis such as finding interacting TSS-enhancer pairs and enhancer clusters, to differential expression analysis and alternative TSS usage. R-code, discussion and references are intertwined to help provide guidelines for future CAGE studies of the same kind.

AB - Cap Analysis of Gene Expression (CAGE) is one of the most popular 5'-end sequencing methods. In a single experiment, CAGE can be used to locate and quantify the expression of both Transcription Start Sites (TSSs) and enhancers. This is workflow is a case study on how to use the CAGEfightR package to orchestrate analysis of CAGE data within the Bioconductor project. This workflow starts from BigWig-files and covers both basic CAGE analyses such as identifying, quantifying and annotating TSSs and enhancers, advanced analysis such as finding interacting TSS-enhancer pairs and enhancer clusters, to differential expression analysis and alternative TSS usage. R-code, discussion and references are intertwined to help provide guidelines for future CAGE studies of the same kind.

U2 - 10.12688/f1000research.18456.1

DO - 10.12688/f1000research.18456.1

M3 - Journal article

C2 - 31327999

VL - 8

JO - F1000Research

JF - F1000Research

SN - 2046-1402

M1 - 886

ER -

ID: 224945711