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 1.9.3
## 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] ggplot2_4.0.0 reshape2_1.4.4 CytoPipeline_1.9.3 BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] changepoint_2.3 tidyselect_1.2.1 dplyr_1.1.4
## [4] farver_2.1.2 blob_1.2.4 filelock_1.0.3
## [7] S7_0.2.0 fastmap_1.2.0 BiocFileCache_2.99.6
## [10] XML_3.99-0.19 digest_0.6.37 lifecycle_1.0.4
## [13] cluster_2.1.8.1 RSQLite_2.4.3 magrittr_2.0.4
## [16] compiler_4.5.1 rlang_1.1.6 sass_0.4.10
## [19] tools_4.5.1 yaml_2.3.10 data.table_1.17.8
## [22] knitr_1.50 labeling_0.4.3 bit_4.6.0
## [25] curl_7.0.0 diagram_1.6.5 plyr_1.8.9
## [28] RColorBrewer_1.1-3 withr_3.0.2 purrr_1.1.0
## [31] RProtoBufLib_2.21.0 BiocGenerics_0.55.1 PeacoQC_1.19.0
## [34] grid_4.5.1 stats4_4.5.1 flowAI_1.39.0
## [37] colorspace_2.1-2 scales_1.4.0 iterators_1.0.14
## [40] tinytex_0.57 dichromat_2.0-0.1 cli_3.6.5
## [43] rmarkdown_2.30 crayon_1.5.3 ncdfFlow_2.55.0
## [46] generics_0.1.4 rjson_0.2.23 DBI_1.2.3
## [49] cachem_1.1.0 flowCore_2.21.0 stringr_1.5.2
## [52] parallel_4.5.1 BiocManager_1.30.26 matrixStats_1.5.0
## [55] vctrs_0.6.5 jsonlite_2.0.0 cytolib_2.21.0
## [58] bookdown_0.44 IRanges_2.43.4 GetoptLong_1.0.5
## [61] S4Vectors_0.47.4 bit64_4.6.0-1 clue_0.3-66
## [64] Rgraphviz_2.53.0 magick_2.9.0 foreach_1.5.2
## [67] jquerylib_0.1.4 hexbin_1.28.5 glue_1.8.0
## [70] codetools_0.2-20 stringi_1.8.7 gtable_0.3.6
## [73] shape_1.4.6.1 ggcyto_1.37.1 ComplexHeatmap_2.25.2
## [76] tibble_3.3.0 pillar_1.11.1 rappdirs_0.3.3
## [79] htmltools_0.5.8.1 graph_1.87.0 circlize_0.4.16
## [82] R6_2.6.1 dbplyr_2.5.1 httr2_1.2.1
## [85] doParallel_1.0.17 evaluate_1.0.5 flowWorkspace_4.21.0
## [88] lattice_0.22-7 Biobase_2.69.1 png_0.1-8
## [91] memoise_2.0.1 bslib_0.9.0 Rcpp_1.1.0
## [94] gridExtra_2.3 xfun_0.53 zoo_1.8-14
## [97] pkgconfig_2.0.3 GlobalOptions_0.1.2