This vignette provides links to videos demonstrating some of the functionalities of CytoPipeline R package suite. It is distributed, as well as the accompanying videos, under a CC BY-SA license.
CytoPipeline 1.9.4
## R version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] patchwork_1.3.2 CytoPipelineGUI_1.7.2 CytoPipeline_1.9.4
## [4] BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] DBI_1.2.3 gridExtra_2.3 httr2_1.2.1
## [4] rlang_1.1.6 magrittr_2.0.4 clue_0.3-66
## [7] GetoptLong_1.0.5 matrixStats_1.5.0 compiler_4.5.1
## [10] RSQLite_2.4.3 png_0.1-8 vctrs_0.6.5
## [13] reshape2_1.4.4 stringr_1.5.2 pkgconfig_2.0.3
## [16] shape_1.4.6.1 crayon_1.5.3 fastmap_1.2.0
## [19] magick_2.9.0 dbplyr_2.5.1 labeling_0.4.3
## [22] promises_1.3.3 ncdfFlow_2.55.0 rmarkdown_2.30
## [25] graph_1.87.0 tinytex_0.57 purrr_1.1.0
## [28] bit_4.6.0 xfun_0.53 cachem_1.1.0
## [31] jsonlite_2.0.0 flowWorkspace_4.21.0 blob_1.2.4
## [34] later_1.4.4 parallel_4.5.1 cluster_2.1.8.1
## [37] R6_2.6.1 bslib_0.9.0 stringi_1.8.7
## [40] RColorBrewer_1.1-3 jquerylib_0.1.4 Rcpp_1.1.0
## [43] bookdown_0.44 iterators_1.0.14 knitr_1.50
## [46] zoo_1.8-14 IRanges_2.43.5 flowCore_2.21.0
## [49] httpuv_1.6.16 tidyselect_1.2.1 dichromat_2.0-0.1
## [52] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
## [55] curl_7.0.0 lattice_0.22-7 tibble_3.3.0
## [58] plyr_1.8.9 Biobase_2.69.1 shiny_1.11.1
## [61] withr_3.0.2 S7_0.2.0 evaluate_1.0.5
## [64] BiocFileCache_2.99.6 circlize_0.4.16 pillar_1.11.1
## [67] BiocManager_1.30.26 filelock_1.0.3 foreach_1.5.2
## [70] flowAI_1.39.0 stats4_4.5.1 generics_0.1.4
## [73] S4Vectors_0.47.4 ggplot2_4.0.0 ggcyto_1.37.1
## [76] scales_1.4.0 xtable_1.8-4 PeacoQC_1.19.0
## [79] glue_1.8.0 changepoint_2.3 tools_4.5.1
## [82] hexbin_1.28.5 data.table_1.17.8 XML_3.99-0.19
## [85] grid_4.5.1 RProtoBufLib_2.21.0 colorspace_2.1-2
## [88] cli_3.6.5 rappdirs_0.3.3 cytolib_2.21.0
## [91] ComplexHeatmap_2.25.2 dplyr_1.1.4 Rgraphviz_2.53.0
## [94] gtable_0.3.6 sass_0.4.10 digest_0.6.37
## [97] BiocGenerics_0.55.1 rjson_0.2.23 farver_2.1.2
## [100] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
## [103] GlobalOptions_0.1.2 mime_0.13 bit64_4.6.0-1