Overview

SPEAQeasy is a Nextflow-based Scalable RNA-seq Pipeline for Expression Analysis and Quantification.

Diagram representing the “conceptual” workflow traversed by SPEAQeasy. Here some nextflow processes are grouped together for simplicity; the exact processes traversed are enumerated here. The red box indicates the FASTQ files are inputs to the pipeline; green coloring denotes major output files from the pipeline; the remaining boxes represent computational steps. Yellow-colored steps are optional or not always performed; for example, preparing a particular set of annotation files occurs once and uses a cache for further runs. Finally, blue-colored steps are ordinary processes which occur on every pipeline execution.

Cite SPEAQeasy

We hope that SPEAQeasy will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

@article {Eagles2021,
    author = {Eagles, Nicholas J. and Burke, Emily E. and Leonard, Jabob and Barry, Brianna K. and Stolz, Joshua M. and Huuki, Louise and Phan, BaDoi N. and Larrios Serrato, Violeta and Guti{\'e}rrez-Mill{\'a}n, Everardo and Aguilar-Ordo{\~n}ez, Israel and Jaffe, Andrew E. and Collado-Torres, Leonardo},
    title = {SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses},
    year = {2021},
    doi = {10.1186/s12859-021-04142-3},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://doi.org/10.1186/s12859-021-04142-3},
    journal = {BMC Bioinformatics}
}

This is a project by the R/Bioconductor-powered Team Data Science at the Lieber Institute for Brain Development.

R session information

Details on the R version used for making this book. The source code is available at LieberInstitute/SPEAQeasy.

## Load the package at the top of your script
library("sessioninfo")

## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
## [1] "Reproducibility information:"
## [1] "2021-05-14 17:38:29 UTC"
##    user  system elapsed 
##   0.480   0.101   0.490
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value                                             
##  version  R Under development (unstable) (2021-04-15 r80175)
##  os       Ubuntu 20.04.2 LTS                                
##  system   x86_64, linux-gnu                                 
##  ui       X11                                               
##  language (EN)                                              
##  collate  en_US.UTF-8                                       
##  ctype    en_US.UTF-8                                       
##  tz       Etc/UTC                                           
##  date     2021-05-14                                        
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package     * version date       lib source        
##  bookdown      0.22    2021-04-22 [1] CRAN (R 4.1.0)
##  cli           2.4.0   2021-04-05 [2] CRAN (R 4.1.0)
##  digest        0.6.27  2020-10-24 [2] CRAN (R 4.1.0)
##  evaluate      0.14    2019-05-28 [2] CRAN (R 4.1.0)
##  glue          1.4.2   2020-08-27 [2] CRAN (R 4.1.0)
##  htmltools     0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
##  knitr         1.32    2021-04-14 [2] CRAN (R 4.1.0)
##  magrittr      2.0.1   2020-11-17 [2] CRAN (R 4.1.0)
##  rlang         0.4.10  2020-12-30 [2] CRAN (R 4.1.0)
##  rmarkdown     2.8     2021-05-07 [1] CRAN (R 4.1.0)
##  rstudioapi    0.13    2020-11-12 [2] CRAN (R 4.1.0)
##  sessioninfo * 1.1.1   2018-11-05 [2] CRAN (R 4.1.0)
##  stringi       1.5.3   2020-09-09 [2] CRAN (R 4.1.0)
##  stringr       1.4.0   2019-02-10 [2] CRAN (R 4.1.0)
##  withr         2.4.1   2021-01-26 [2] CRAN (R 4.1.0)
##  xfun          0.22    2021-03-11 [2] CRAN (R 4.1.0)
##  yaml          2.2.1   2020-02-01 [2] CRAN (R 4.1.0)
## 
## [1] /usr/local/lib/R/host-site-library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library

This book was last updated on 2021-05-14 17:38:29.