# Chevreul

# Basics

## Install `chevreulPlot`

`R` is an open-source statistical environment which can be easily modified to enhance its functionality via packages. chevreulPlot is a `R` package available via the Bioconductor repository for packages. `R` can be installed on any operating system from CRAN after which you can install chevreulPlot by using the following commands in your `R` session:

    if (!requireNamespace("BiocManager", quietly = TRUE)) {
        install.packages("BiocManager")
    }

    BiocManager::install("chevreulPlot")

## Required knowledge

The chevreulPlot package is designed for single-cell RNA sequencing data. The functions included within this package are derived from other packages that have implemented the infrastructure needed for RNA-seq data processing and analysis. Packages that have been instrumental in the development of chevreulPlot include, `Biocpkg("SummarizedExperiment")` and `Biocpkg("scater")`.

## Asking for help

`R` and `Bioconductor` have a steep learning curve so it is critical to learn where to ask for help. The Bioconductor support site is the main resource for getting help: remember to use the `chevreulPlot` tag and check the older posts.

# Quick start to using `chevreulPlot`

The `chevreulPlot` package contains functions to preprocess, cluster, visualize, and perform other analyses on scRNA-seq data. It also contains a shiny app for easy visualization and analysis of scRNA data.

`chvereul` uses SingelCellExperiment (SCE) object type (from SingleCellExperiment) to store expression and other metadata from single-cell experiments.

This package features functions capable of:

- Performing Clustering at a range of resolutions and Dimensional reduction of Raw Sequencing Data.
- Visualizing scRNA data using different plotting functions.
- Integration of multiple datasets for consistent analyses.
- Cell cycle state regression and labeling.

    library("chevreulPlot")

    # Load the data
    data("small_example_dataset")

    sessionInfo()
    #> R version 4.6.0 (2026-04-24)
    #> Platform: x86_64-pc-linux-gnu
    #> Running under: Ubuntu 24.04.4 LTS
    #>
    #> Matrix products: default
    #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    #>
    #> locale:
    #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    #>  [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: Etc/UTC
    #> tzcode source: system (glibc)
    #>
    #> attached base packages:
    #> [1] stats4    stats     graphics  grDevices utils     datasets  methods
    #> [8] base
    #>
    #> other attached packages:
    #>  [1] chevreulPlot_1.5.0          chevreulProcess_1.5.0
    #>  [3] scater_1.41.1               ggplot2_4.0.3
    #>  [5] scuttle_1.23.1              SingleCellExperiment_1.35.1
    #>  [7] SummarizedExperiment_1.43.0 Biobase_2.73.1
    #>  [9] GenomicRanges_1.65.0        Seqinfo_1.3.0
    #> [11] IRanges_2.47.1              S4Vectors_0.51.3
    #> [13] BiocGenerics_0.59.6         generics_0.1.4
    #> [15] MatrixGenerics_1.25.0       matrixStats_1.5.0
    #> [17] BiocStyle_2.41.0
    #>
    #> loaded via a namespace (and not attached):
    #>   [1] RColorBrewer_1.1-3        sys_3.4.3
    #>   [3] jsonlite_2.0.0            shape_1.4.6.1
    #>   [5] magrittr_2.0.5            ggbeeswarm_0.7.3
    #>   [7] GenomicFeatures_1.65.0    farver_2.1.2
    #>   [9] rmarkdown_2.31            GlobalOptions_0.1.4
    #>  [11] fs_2.1.0                  BiocIO_1.23.3
    #>  [13] vctrs_0.7.3               memoise_2.0.1
    #>  [15] Rsamtools_2.29.0          DelayedMatrixStats_1.35.0
    #>  [17] RCurl_1.98-1.18           forcats_1.0.1
    #>  [19] htmltools_0.5.9           S4Arrays_1.13.0
    #>  [21] BiocBaseUtils_1.15.1      curl_7.1.0
    #>  [23] BiocNeighbors_2.7.2       SparseArray_1.13.2
    #>  [25] sass_0.4.10               bslib_0.11.0
    #>  [27] htmlwidgets_1.6.4         plotly_4.12.0
    #>  [29] cachem_1.1.0              ResidualMatrix_1.23.0
    #>  [31] buildtools_1.0.0          GenomicAlignments_1.49.0
    #>  [33] igraph_2.3.1              iterators_1.0.14
    #>  [35] lifecycle_1.0.5           pkgconfig_2.0.3
    #>  [37] rsvd_1.0.5                Matrix_1.7-5
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    #>  [41] clue_0.3-68               digest_0.6.39
    #>  [43] colorspace_2.1-2          patchwork_1.3.2
    #>  [45] AnnotationDbi_1.75.0      dqrng_0.4.1
    #>  [47] irlba_2.3.7               RSQLite_3.53.1
    #>  [49] beachmat_2.29.0           httr_1.4.8
    #>  [51] abind_1.4-8               compiler_4.6.0
    #>  [53] doParallel_1.0.17         bit64_4.8.2
    #>  [55] withr_3.0.2               S7_0.2.2
    #>  [57] BiocParallel_1.47.0       viridis_0.6.5
    #>  [59] DBI_1.3.0                 DelayedArray_0.39.3
    #>  [61] rjson_0.2.23              bluster_1.23.0
    #>  [63] tools_4.6.0               vipor_0.4.7
    #>  [65] otel_0.2.0                beeswarm_0.4.0
    #>  [67] glue_1.8.1                restfulr_0.0.16
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    #>  [71] cluster_2.1.8.2           megadepth_1.23.0
    #>  [73] gtable_0.3.6              tzdb_0.5.0
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    #>  [77] data.table_1.18.4         hms_1.1.4
    #>  [79] metapod_1.21.0            BiocSingular_1.29.0
    #>  [81] ScaledMatrix_1.21.0       XVector_0.53.0
    #>  [83] foreach_1.5.2             stringr_1.6.0
    #>  [85] ggrepel_0.9.8             pillar_1.11.1
    #>  [87] limma_3.69.1              circlize_0.4.18
    #>  [89] dplyr_1.2.1               lattice_0.22-9
    #>  [91] rtracklayer_1.73.0        bit_4.6.0
    #>  [93] tidyselect_1.2.1          ComplexHeatmap_2.29.0
    #>  [95] locfit_1.5-9.12           maketools_1.3.2
    #>  [97] Biostrings_2.81.2         knitr_1.51
    #>  [99] gridExtra_2.3             ProtGenerics_1.45.0
    #> [101] edgeR_4.11.1              cmdfun_1.0.2
    #> [103] xfun_0.57                 statmod_1.5.2
    #> [105] stringi_1.8.7             UCSC.utils_1.9.0
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    #> [109] yaml_2.3.12               evaluate_1.0.5
    #> [111] codetools_0.2-20          cigarillo_1.3.0
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    #> [115] BiocManager_1.30.27       cli_3.6.6
    #> [117] jquerylib_0.1.4           Rcpp_1.1.1-1.1
    #> [119] GenomeInfoDb_1.49.1       png_0.1-9
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    #> [123] readr_2.2.0               blob_1.3.0
    #> [125] AnnotationFilter_1.37.0   scran_1.41.1
    #> [127] sparseMatrixStats_1.25.0  bitops_1.0-9
    #> [129] viridisLite_0.4.3         scales_1.4.0
    #> [131] purrr_1.2.2               crayon_1.5.3
    #> [133] GetoptLong_1.1.1          rlang_1.2.0
    #> [135] KEGGREST_1.53.0