Skip to main content
Download PDF

Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses

BMC Bioinformatics volume 22, Article number: 381 (2021) Cite this article

The Original Article was published on 01 May 2021

Correction to: BMC Bioinformatics (2021) 22:224 https://doi.org/10.1186/s12859-021-04142-3

Following the publication of the original article [1], the authors identified the incorrect published Additional file 4 and missing Additional file 1: figures S1 and Additional file 2: S2.

The original article [1] has been corrected.

Reference

  1. Eagles NJ, et al. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinformatics. 2021;22:224. https://doi.org/10.1186/s12859-021-04142-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA

    Nicholas J. Eagles, Emily E. Burke, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Andrew E. Jaffe & Leonardo Collado-Torres

  2. Winter Genomics, Salaverry 874 int 100, Lindavista, CDMX, 07300, Mexico

    Jacob Leonard, Violeta Larios Serrato, Everardo Gutiérrez-Millán & Israel Aguilar-Ordoñez

  3. QuestBridge Scholar, Palo Alto, CA, 94303, USA

    Jacob Leonard

  4. Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA

    Brianna K. Barry & Andrew E. Jaffe

  5. Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA

    BaDoi N. Phan

  6. Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA

    BaDoi N. Phan

  7. Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas,, Mexico City, CDMX, 11340, Mexico

    Violeta Larios Serrato

  8. Department of Supercomputing, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, CDMX, 14610, Mexico

    Israel Aguilar-Ordoñez

  9. Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA

    Andrew E. Jaffe & Leonardo Collado-Torres

  10. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA

    Andrew E. Jaffe

  11. Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

    Andrew E. Jaffe

  12. Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA

    Andrew E. Jaffe

  13. Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA

    Andrew E. Jaffe

Authors
  1. Nicholas J. Eagles
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emily E. Burke
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jacob Leonard
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Brianna K. Barry
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Joshua M. Stolz
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Louise Huuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. BaDoi N. Phan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Violeta Larios Serrato
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Everardo Gutiérrez-Millán
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Israel Aguilar-Ordoñez
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Andrew E. Jaffe
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Leonardo Collado-Torres
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Leonardo Collado-Torres.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1

: Figure S1. Expected vs. Actual ERCC concentration. SPEAQeasy produces plots for each sample, for easy visual comparison of expected ERCC transcript abundance with the kallisto-measured concentration.

Additional file 2

: Figure S2. SPEAQeasy logs tracing computational steps by sample. To aid transparency and greatly simplify the source of execution errors, SPEAQeasy automatically generates logs with several pieces of information for every sample. In order of submission, the name of each Nextflow process is printed, along with (1) the working directory: where all relevant files are present, (2) the exit code: a standard indication of whether the process succeeded or how it failed, (3) a list of the specific commands run during the given process. Above is a snapshot of the top of an example log

Additional file 4

: SNVs supplementary BED files. The common SNVs used for sample identification are stored in the BED files (A) common_missense_SNVs_hg19.bed and (B) common_missense_SNVs_hg38.bed.

Additional file 4

: SNVs supplementary BED files. The common SNVs used for sample identification are stored in the BED files (A) common_missense_SNVs_hg19.bed and (B) common_missense_SNVs_hg38.bed.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Eagles, N.J., Burke, E.E., Leonard, J. et al. Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. BMC Bioinformatics 22, 381 (2021). https://doi.org/10.1186/s12859-021-04283-5

Download citation

  • Published:

  • DOI: https://doi.org/10.1186/s12859-021-04283-5

BMC Bioinformatics

ISSN: 1471-2105

Contact us