Started on 2025-02-07 09:42:28

Mpileup

Sample Clustering

Variants by Chromosomes

Input Dataset

SessionInfo

## ezRun tag: ed29b51d935a7281b59ff7ca5e23d187e8f449d3 
## ezRun github link: https://github.com/uzh/ezRun/tree/ed29b51d935a7281b59ff7ca5e23d187e8f449d3 
##  
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Debian GNU/Linux 12 (bookworm)
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
## 
## 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: Europe/Zurich
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] htmltools_0.5.8.1           DT_0.33                    
##  [3] RColorBrewer_1.1-3          readxl_1.4.3               
##  [5] htmlwidgets_1.6.4           webshot_0.5.5              
##  [7] plotly_4.10.4               kableExtra_1.4.0           
##  [9] knitr_1.49                  qs2_0.1.4                  
## [11] VariantAnnotation_1.52.0    Rsamtools_2.22.0           
## [13] SummarizedExperiment_1.36.0 Biobase_2.66.0             
## [15] MatrixGenerics_1.18.0       matrixStats_1.4.1          
## [17] ezRun_3.20.1                lubridate_1.9.4            
## [19] forcats_1.0.0               stringr_1.5.1              
## [21] dplyr_1.1.4                 purrr_1.0.2                
## [23] readr_2.1.5                 tidyr_1.3.1                
## [25] tibble_3.2.1                ggplot2_3.5.1              
## [27] tidyverse_2.0.0             GenomicRanges_1.58.0       
## [29] Biostrings_2.74.0           GenomeInfoDb_1.42.1        
## [31] XVector_0.46.0              IRanges_2.40.1             
## [33] S4Vectors_0.44.0            BiocGenerics_0.52.0        
## [35] data.table_1.16.4          
## 
## loaded via a namespace (and not attached):
##  [1] DBI_1.2.3                bitops_1.0-9             rlang_1.1.4             
##  [4] magrittr_2.0.3           compiler_4.4.2           RSQLite_2.3.9           
##  [7] GenomicFeatures_1.58.0   png_0.1-8                systemfonts_1.1.0       
## [10] vctrs_0.6.5              pkgconfig_2.0.3          crayon_1.5.3            
## [13] fastmap_1.2.0            rmarkdown_2.29           tzdb_0.4.0              
## [16] UCSC.utils_1.2.0         bit_4.5.0.1              xfun_0.49               
## [19] zlibbioc_1.52.0          cachem_1.1.0             jsonlite_1.8.9          
## [22] blob_1.2.4               DelayedArray_0.32.0      BiocParallel_1.40.0     
## [25] R6_2.5.1                 bslib_0.8.0              stringi_1.8.4           
## [28] rtracklayer_1.66.0       cellranger_1.1.0         jquerylib_0.1.4         
## [31] Rcpp_1.0.13.6            Matrix_1.7-1             timechange_0.3.0        
## [34] tidyselect_1.2.1         rstudioapi_0.17.1        abind_1.4-8             
## [37] yaml_2.3.10              stringfish_0.16.0        codetools_0.2-20        
## [40] curl_6.0.1               lattice_0.22-6           withr_3.0.2             
## [43] KEGGREST_1.46.0          evaluate_1.0.1           RcppParallel_5.1.9      
## [46] xml2_1.3.6               pillar_1.10.0            generics_0.1.3          
## [49] RCurl_1.98-1.16          hms_1.1.3                munsell_0.5.1           
## [52] scales_1.3.0             glue_1.8.0               lazyeval_0.2.2          
## [55] tools_4.4.2              BiocIO_1.16.0            BSgenome_1.74.0         
## [58] GenomicAlignments_1.42.0 XML_3.99-0.17            grid_4.4.2              
## [61] crosstalk_1.2.1          AnnotationDbi_1.68.0     colorspace_2.1-1        
## [64] GenomeInfoDbData_1.2.13  restfulr_0.0.15          cli_3.6.3               
## [67] S4Arrays_1.6.0           viridisLite_0.4.2        svglite_2.1.3           
## [70] gtable_0.3.6             sass_0.4.9               digest_0.6.37           
## [73] SparseArray_1.6.0        rjson_0.2.23             memoise_2.0.1           
## [76] lifecycle_1.0.4          httr_1.4.7               bit64_4.5.2