Basics

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

BiocManager::install("chevreulProcess")

Quick start to using chevreulProcess

The chevreulProcess 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("chevreulProcess")

# Load the data
data("small_example_dataset")

R session information.

#> 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] chevreulProcess_1.5.0       scater_1.41.1              
#>  [3] ggplot2_4.0.3               scuttle_1.23.0             
#>  [5] SingleCellExperiment_1.35.1 SummarizedExperiment_1.43.0
#>  [7] Biobase_2.73.1              GenomicRanges_1.65.0       
#>  [9] Seqinfo_1.3.0               IRanges_2.47.0             
#> [11] S4Vectors_0.51.1            BiocGenerics_0.59.1        
#> [13] generics_0.1.4              MatrixGenerics_1.25.0      
#> [15] matrixStats_1.5.0           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           htmltools_0.5.9          
#>  [19] S4Arrays_1.13.0           BiocBaseUtils_1.15.1     
#>  [21] curl_7.1.0                BiocNeighbors_2.7.2      
#>  [23] SparseArray_1.13.2        sass_0.4.10              
#>  [25] bslib_0.10.0              cachem_1.1.0             
#>  [27] ResidualMatrix_1.23.0     buildtools_1.0.0         
#>  [29] GenomicAlignments_1.49.0  igraph_2.3.1             
#>  [31] lifecycle_1.0.5           pkgconfig_2.0.3          
#>  [33] rsvd_1.0.5                Matrix_1.7-5             
#>  [35] R6_2.6.1                  fastmap_1.2.0            
#>  [37] digest_0.6.39             colorspace_2.1-2         
#>  [39] AnnotationDbi_1.75.0      dqrng_0.4.1              
#>  [41] irlba_2.3.7               RSQLite_3.52.0           
#>  [43] beachmat_2.29.0           httr_1.4.8               
#>  [45] abind_1.4-8               compiler_4.6.0           
#>  [47] bit64_4.8.0               withr_3.0.2              
#>  [49] S7_0.2.2                  BiocParallel_1.47.0      
#>  [51] viridis_0.6.5             DBI_1.3.0                
#>  [53] DelayedArray_0.39.1       rjson_0.2.23             
#>  [55] bluster_1.23.0            tools_4.6.0              
#>  [57] vipor_0.4.7               beeswarm_0.4.0           
#>  [59] glue_1.8.1                restfulr_0.0.16          
#>  [61] batchelor_1.29.0          grid_4.6.0               
#>  [63] cluster_2.1.8.2           megadepth_1.23.0         
#>  [65] gtable_0.3.6              tzdb_0.5.0               
#>  [67] ensembldb_2.37.0          hms_1.1.4                
#>  [69] metapod_1.21.0            BiocSingular_1.29.0      
#>  [71] ScaledMatrix_1.21.0       XVector_0.53.0           
#>  [73] stringr_1.6.0             ggrepel_0.9.8            
#>  [75] pillar_1.11.1             limma_3.69.0             
#>  [77] circlize_0.4.18           dplyr_1.2.1              
#>  [79] lattice_0.22-9            rtracklayer_1.73.0       
#>  [81] bit_4.6.0                 tidyselect_1.2.1         
#>  [83] locfit_1.5-9.12           maketools_1.3.2          
#>  [85] Biostrings_2.81.1         knitr_1.51               
#>  [87] gridExtra_2.3             ProtGenerics_1.45.0      
#>  [89] edgeR_4.11.0              cmdfun_1.0.2             
#>  [91] xfun_0.57                 statmod_1.5.1            
#>  [93] stringi_1.8.7             UCSC.utils_1.9.0         
#>  [95] EnsDb.Hsapiens.v86_2.99.0 lazyeval_0.2.3           
#>  [97] yaml_2.3.12               evaluate_1.0.5           
#>  [99] codetools_0.2-20          cigarillo_1.3.0          
#> [101] tibble_3.3.1              BiocManager_1.30.27      
#> [103] cli_3.6.6                 jquerylib_0.1.4          
#> [105] Rcpp_1.1.1-1.1            GenomeInfoDb_1.49.0      
#> [107] png_0.1-9                 XML_3.99-0.23            
#> [109] parallel_4.6.0            readr_2.2.0              
#> [111] blob_1.3.0                AnnotationFilter_1.37.0  
#> [113] scran_1.41.0              sparseMatrixStats_1.25.0 
#> [115] bitops_1.0-9              viridisLite_0.4.3        
#> [117] scales_1.4.0              purrr_1.2.2              
#> [119] crayon_1.5.3              rlang_1.2.0              
#> [121] KEGGREST_1.53.0