RNA-Seq workflow: gene-level exploratory analysis and differential expression

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene...

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Detalles Bibliográficos
Autores principales: Love, Michael I., Anders, Simon, Kim, Vladislav, Huber, Wolfgang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2015
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670015/
https://www.ncbi.nlm.nih.gov/pubmed/26674615
http://dx.doi.org/10.12688/f1000research.7035.1
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author Love, Michael I.
Anders, Simon
Kim, Vladislav
Huber, Wolfgang
author_facet Love, Michael I.
Anders, Simon
Kim, Vladislav
Huber, Wolfgang
author_sort Love, Michael I.
collection PubMed
description Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.
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spelling pubmed-46700152015-12-14 RNA-Seq workflow: gene-level exploratory analysis and differential expression Love, Michael I. Anders, Simon Kim, Vladislav Huber, Wolfgang F1000Res Research Article Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results. F1000Research 2015-10-14 /pmc/articles/PMC4670015/ /pubmed/26674615 http://dx.doi.org/10.12688/f1000research.7035.1 Text en Copyright: © 2015 Love MI et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Love, Michael I.
Anders, Simon
Kim, Vladislav
Huber, Wolfgang
RNA-Seq workflow: gene-level exploratory analysis and differential expression
title RNA-Seq workflow: gene-level exploratory analysis and differential expression
title_full RNA-Seq workflow: gene-level exploratory analysis and differential expression
title_fullStr RNA-Seq workflow: gene-level exploratory analysis and differential expression
title_full_unstemmed RNA-Seq workflow: gene-level exploratory analysis and differential expression
title_short RNA-Seq workflow: gene-level exploratory analysis and differential expression
title_sort rna-seq workflow: gene-level exploratory analysis and differential expression
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670015/
https://www.ncbi.nlm.nih.gov/pubmed/26674615
http://dx.doi.org/10.12688/f1000research.7035.1
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