1 Redirect notification

The systemPipeRdata package provides a collection of pre-built workflow templates that are ready to use from systemPipeR. These templates are described in detail in the associated systemPipeRdata overview vignette here, which includes instructions on how to use them.

2 Funding

This project is funded by awards from the National Science Foundation (ABI-1661152), and the National Institute on Aging of the National Institutes of Health (U19AG023122).

3 Session Info

sessionInfo()
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] magrittr_2.0.5           systemPipeR_2.19.8       ShortRead_1.71.1        
##  [4] GenomicAlignments_1.49.2 BiocParallel_1.47.0      Rsamtools_2.29.0        
##  [7] Biostrings_2.81.9        XVector_0.53.0           GenomicRanges_1.65.4    
## [10] IRanges_2.47.5           S4Vectors_0.51.10        Seqinfo_1.3.2           
## [13] BiocGenerics_0.59.12     generics_0.1.4           BiocStyle_2.41.0        
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.1            viridisLite_0.4.3          
##  [3] dplyr_1.2.1                 farver_2.1.2               
##  [5] S7_0.2.2                    bitops_1.1-0               
##  [7] fastmap_1.2.0               digest_0.6.39              
##  [9] lifecycle_1.0.5             pwalign_1.9.1              
## [11] compiler_4.6.1              rlang_1.3.0                
## [13] sass_0.4.10                 tools_4.6.1                
## [15] yaml_2.3.12                 knitr_1.52                 
## [17] S4Arrays_1.13.2             labeling_0.4.3             
## [19] htmlwidgets_1.6.4           interp_1.1-6               
## [21] DelayedArray_0.39.8         xml2_1.6.0                 
## [23] RColorBrewer_1.1-3          abind_1.4-8                
## [25] withr_3.0.3                 hwriter_1.3.2.1            
## [27] grid_4.6.1                  latticeExtra_0.6-31        
## [29] ggplot2_4.0.3               scales_1.4.0               
## [31] dichromat_2.0-1             tinytex_0.61               
## [33] SummarizedExperiment_1.43.0 cli_3.6.6                  
## [35] rmarkdown_2.32              crayon_1.5.3               
## [37] otel_0.2.0                  rstudioapi_0.19.0          
## [39] cachem_1.1.0                stringr_1.6.0              
## [41] parallel_4.6.1              formatR_1.14               
## [43] BiocManager_1.30.27         matrixStats_1.5.0          
## [45] vctrs_0.7.3                 Matrix_1.7-6               
## [47] jsonlite_2.0.0              bookdown_0.48              
## [49] systemfonts_1.3.2           jpeg_0.1-11                
## [51] magick_2.9.1                crosstalk_1.2.2            
## [53] jquerylib_0.1.4             glue_1.8.1                 
## [55] codetools_0.2-20            DT_0.34.0                  
## [57] stringi_1.8.9               gtable_0.3.6               
## [59] deldir_2.0-4                tibble_3.3.1               
## [61] pillar_1.11.1               htmltools_0.5.9            
## [63] R6_2.6.1                    textshaping_1.0.5          
## [65] evaluate_1.0.5              kableExtra_1.4.1           
## [67] lattice_0.23-1              Biobase_2.73.2             
## [69] png_0.1-9                   cigarillo_1.3.1            
## [71] bslib_0.12.0                Rcpp_1.1.2                 
## [73] svglite_2.2.2               SparseArray_1.13.4         
## [75] xfun_0.62                   MatrixGenerics_1.25.0      
## [77] pkgconfig_2.0.3