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 4.4.3 (2025-02-28)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 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=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: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] chevreulProcess_0.99.27     scater_1.35.4              
#>  [3] ggplot2_3.5.1               scuttle_1.17.0             
#>  [5] SingleCellExperiment_1.29.2 SummarizedExperiment_1.37.0
#>  [7] Biobase_2.67.0              GenomicRanges_1.59.1       
#>  [9] GenomeInfoDb_1.43.4         IRanges_2.41.3             
#> [11] S4Vectors_0.45.4            BiocGenerics_0.53.6        
#> [13] generics_0.1.3              MatrixGenerics_1.19.1      
#> [15] matrixStats_1.5.0           BiocStyle_2.35.0           
#> 
#> loaded via a namespace (and not attached):
#>   [1] sys_3.4.3                 jsonlite_1.9.1           
#>   [3] shape_1.4.6.1             magrittr_2.0.3           
#>   [5] ggbeeswarm_0.7.2          GenomicFeatures_1.59.1   
#>   [7] rmarkdown_2.29            GlobalOptions_0.1.2      
#>   [9] fs_1.6.5                  BiocIO_1.17.1            
#>  [11] vctrs_0.6.5               memoise_2.0.1            
#>  [13] Rsamtools_2.23.1          DelayedMatrixStats_1.29.1
#>  [15] RCurl_1.98-1.16           htmltools_0.5.8.1        
#>  [17] S4Arrays_1.7.3            curl_6.2.1               
#>  [19] BiocNeighbors_2.1.3       SparseArray_1.7.6        
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#>  [25] buildtools_1.0.0          GenomicAlignments_1.43.0 
#>  [27] igraph_2.1.4              lifecycle_1.0.4          
#>  [29] pkgconfig_2.0.3           rsvd_1.0.5               
#>  [31] Matrix_1.7-3              R6_2.6.1                 
#>  [33] fastmap_1.2.0             GenomeInfoDbData_1.2.13  
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#>  [39] irlba_2.3.5.1             RSQLite_2.3.9            
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#>  [43] abind_1.4-8               compiler_4.4.3           
#>  [45] bit64_4.6.0-1             withr_3.0.2              
#>  [47] BiocParallel_1.41.2       viridis_0.6.5            
#>  [49] DBI_1.2.3                 DelayedArray_0.33.6      
#>  [51] rjson_0.2.23              bluster_1.17.0           
#>  [53] tools_4.4.3               vipor_0.4.7              
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#>  [57] restfulr_0.0.15           batchelor_1.23.1         
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#>  [75] dplyr_1.1.4               lattice_0.22-6           
#>  [77] rtracklayer_1.67.1        bit_4.6.0                
#>  [79] tidyselect_1.2.1          locfit_1.5-9.12          
#>  [81] maketools_1.3.2           Biostrings_2.75.4        
#>  [83] knitr_1.49                gridExtra_2.3            
#>  [85] ProtGenerics_1.39.2       edgeR_4.5.9              
#>  [87] cmdfun_1.0.2              xfun_0.51                
#>  [89] statmod_1.5.0             stringi_1.8.4            
#>  [91] UCSC.utils_1.3.1          EnsDb.Hsapiens.v86_2.99.0
#>  [93] lazyeval_0.2.2            yaml_2.3.10              
#>  [95] evaluate_1.0.3            codetools_0.2-20         
#>  [97] tibble_3.2.1              BiocManager_1.30.25      
#>  [99] cli_3.6.4                 munsell_0.5.1            
#> [101] jquerylib_0.1.4           Rcpp_1.0.14              
#> [103] png_0.1-8                 XML_3.99-0.18            
#> [105] parallel_4.4.3            readr_2.1.5              
#> [107] blob_1.2.4                AnnotationFilter_1.31.0  
#> [109] scran_1.35.0              sparseMatrixStats_1.19.0 
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