Overview

PopTop is a Nextflow-based Pipeline of Parallelized for Topmed Imputation.

Diagram representing the “conceptual” workflow traversed by PopTop. Here some nextflow processes are are simplified for visualization; the exact processes traversed are enumerated here

Cite PopTop

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

@article {Eagles2021,
    author = {Stolz, Joshua M. and Eagles, Nicholas J. and Jaffe, Andrew E. and Collado-Torres, Leonardo},
    title = {PopTop: Pipeline of Parallelized TopMed Imputation},
    year = {2022}
}

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/Topmed-Imputation-Pipeline.

## 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] "2023-11-27 03:40:35 UTC"
##    user  system elapsed 
##   0.688   0.142   0.784
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R Under development (unstable) (2023-11-22 r85609)
##  os       Ubuntu 22.04.3 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       UTC
##  date     2023-11-27
##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package     * version date (UTC) lib source
##  bookdown      0.36    2023-10-16 [1] CRAN (R 4.4.0)
##  bslib         0.6.0   2023-11-21 [2] CRAN (R 4.4.0)
##  cachem        1.0.8   2023-05-01 [2] CRAN (R 4.4.0)
##  cli           3.6.1   2023-03-23 [2] CRAN (R 4.4.0)
##  digest        0.6.33  2023-07-07 [2] CRAN (R 4.4.0)
##  evaluate      0.23    2023-11-01 [2] CRAN (R 4.4.0)
##  fastmap       1.1.1   2023-02-24 [2] CRAN (R 4.4.0)
##  htmltools     0.5.7   2023-11-03 [2] CRAN (R 4.4.0)
##  jquerylib     0.1.4   2021-04-26 [2] CRAN (R 4.4.0)
##  jsonlite      1.8.7   2023-06-29 [2] CRAN (R 4.4.0)
##  knitr         1.45    2023-10-30 [2] CRAN (R 4.4.0)
##  lifecycle     1.0.4   2023-11-07 [2] CRAN (R 4.4.0)
##  R6            2.5.1   2021-08-19 [2] CRAN (R 4.4.0)
##  rlang         1.1.2   2023-11-04 [2] CRAN (R 4.4.0)
##  rmarkdown     2.25    2023-09-18 [2] CRAN (R 4.4.0)
##  rstudioapi    0.15.0  2023-07-07 [2] CRAN (R 4.4.0)
##  sass          0.4.7   2023-07-15 [2] CRAN (R 4.4.0)
##  sessioninfo * 1.2.2   2021-12-06 [2] CRAN (R 4.4.0)
##  xfun          0.41    2023-11-01 [2] CRAN (R 4.4.0)
##  yaml          2.3.7   2023-01-23 [2] CRAN (R 4.4.0)
## 
##  [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 2023-11-27 03:40:35.385381.