Issue reading zscape_perturb_cds.RDS

[Evenlyeven]

Hi,

Thanks for making this amazing dataset available!

I’m running into an issue when trying to read the zscape_perturb_cds.RDS file. Could you please share the md5sum for the file so I can verify that my download completed correctly?

On a side note, the zscape_temp_cds.rds file works.

Here’s the code and error I encountered:

library(monocle3)

# Load the zebrafish perturbation data
perturb_cds <- readRDS("zscape_perturb_cds.RDS")

Error in readRDS("zscape_perturb_cds.RDS") : 
  error reading from connection

My session information:

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Chicago
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] monocle3_1.3.7              SingleCellExperiment_1.28.1 SummarizedExperiment_1.36.0 GenomicRanges_1.58.0       
 [5] GenomeInfoDb_1.42.3         IRanges_2.40.1              S4Vectors_0.44.0            MatrixGenerics_1.18.1      
 [9] matrixStats_1.5.0           Biobase_2.66.0              BiocGenerics_0.52.0        

loaded via a namespace (and not attached):
  [1] fs_1.6.6                 spatstat.sparse_3.1-0    bitops_1.0-9             devtools_2.4.5           lubridate_1.9.4         
  [6] httr_1.4.7               RColorBrewer_1.1-3       profvis_0.4.0            tools_4.4.1              sctransform_0.4.2       
 [11] backports_1.5.0          R6_2.6.1                 sm_2.2-6.0               lazyeval_0.2.2           uwot_0.2.3              
 [16] urlchecker_1.0.1         withr_3.0.2              sp_2.2-0                 gridExtra_2.3            tictoc_1.2.1            
 [21] scCustomize_3.0.1        VennDiagram_1.7.3        progressr_0.15.1         cli_3.6.5                formatR_1.14            
 [26] spatstat.explore_3.4-3   fastDummies_1.7.5        MarkdownHelpers_1.1.1    ggExpress_0.9.5          Seurat_5.3.0            
 [31] spatstat.data_3.1-6      readr_2.1.5              ggridges_0.5.6           pbapply_1.7-2            colorRamps_2.3.4        
 [36] R.utils_2.13.0           harmony_1.2.3            dichromat_2.0-0.1        vioplot_0.5.1            parallelly_1.45.0       
 [41] sessioninfo_1.2.3        rstudioapi_0.17.1        generics_0.1.4           ggVennDiagram_1.5.2      shape_1.4.6.1           
 [46] RApiSerialize_0.1.4      gtools_3.9.5             ica_1.0-3                spatstat.random_3.4-1    dplyr_1.1.4             
 [51] zip_2.3.3                Matrix_1.7-3             futile.logger_1.4.3      ggbeeswarm_0.7.2         clipr_0.8.0             
 [56] abind_1.4-8              R.methodsS3_1.8.2        lifecycle_1.0.4          yaml_2.3.10              snakecase_0.11.1        
 [61] SparseArray_1.6.2        gplots_3.2.0             Rtsne_0.17               paletteer_1.6.0          grid_4.4.1              
 [66] promises_1.3.3           crayon_1.5.3             miniUI_0.1.2             lattice_0.22-7           cowplot_1.1.3           
 [71] pillar_1.10.2            knitr_1.50               boot_1.3-31              future.apply_1.11.3      codetools_0.2-20        
 [76] glue_1.8.0               spatstat.univar_3.1-3    remotes_2.5.0            data.table_1.17.4        Rdpack_2.6.4            
 [81] vctrs_0.6.5              png_0.1-8                EnhancedVolcano_1.24.0   spam_2.11-1              gtable_0.3.6            
 [86] rematch2_2.1.2           CodeAndRoll2_2.7.0       cachem_1.1.0             xfun_0.52                openxlsx_4.2.8          
 [91] rbibutils_2.3            S4Arrays_1.6.0           princurve_2.1.6          mime_0.13                ReadWriter_1.6.0        
 [96] tidyverse_2.0.0          reformulas_0.4.1         survival_3.8-3           pheatmap_1.0.13          iterators_1.0.14        
[101] ellipsis_0.3.2           fitdistrplus_1.2-2       ROCR_1.0-11              nlme_3.1-168             usethis_3.1.0           
[106] Seurat.utils_2.8.5       bit64_4.6.0-1            RcppAnnoy_0.0.22         irlba_2.3.5.1            vipor_0.4.7             
[111] KernSmooth_2.23-26       splitstackshape_1.4.8    SeuratDisk_0.0.0.9021    colorspace_2.1-1         ggrastr_1.0.2           
[116] tidyselect_1.2.1         bit_4.6.0                compiler_4.4.1           hdf5r_1.3.12             DelayedArray_0.32.0     
[121] plotly_4.10.4            stringfish_0.16.0        checkmate_2.3.2          scales_1.4.0             caTools_1.18.3          
[126] lmtest_0.9-40            stringr_1.5.1            digest_0.6.37            goftest_1.2-3            minqa_1.2.8             
[131] spatstat.utils_3.1-4     rmarkdown_2.29           XVector_0.46.0           htmltools_0.5.8.1        pkgconfig_2.0.3         
[136] lme4_1.1-37              sparseMatrixStats_1.18.0 fastmap_1.2.0            rlang_1.1.6              GlobalOptions_0.1.2     
[141] htmlwidgets_1.6.4        UCSC.utils_1.2.0         shiny_1.10.0             farver_2.1.2             zoo_1.8-14              
[146] jsonlite_2.0.0           R.oo_1.27.1              magrittr_2.0.3           GenomeInfoDbData_1.2.13  dotCall64_1.2           
[151] patchwork_1.3.0          Rcpp_1.0.14              reticulate_1.42.0        stringi_1.8.7            zlibbioc_1.52.0         
[156] MASS_7.3-65              pkgbuild_1.4.8           plyr_1.8.9               parallel_4.4.1           listenv_0.9.1           
[161] ggrepel_0.9.6            forcats_1.0.0            MarkdownReports_4.8.0    deldir_2.0-4             splines_4.4.1           
[166] tensor_1.5               hms_1.1.3                circlize_0.4.16          igraph_2.1.4             spatstat.geom_3.4-1     
[171] RcppHNSW_0.6.0           pkgload_1.4.0            reshape2_1.4.4           qs2_0.1.5                futile.options_1.0.1    
[176] evaluate_1.0.3           SeuratObject_5.1.0       RcppParallel_5.1.10      lambda.r_1.2.4           ggprism_1.0.6           
[181] nloptr_2.2.1             tzdb_0.5.0               schard_0.0.1             foreach_1.5.2            httpuv_1.6.16           
[186] RANN_2.6.2               tidyr_1.3.1              purrr_1.0.4              polyclip_1.10-7          qs_0.27.3               
[191] future_1.58.0            scattermore_1.2          ggplot2_3.5.2            janitor_2.2.1            xtable_1.8-4            
[196] RSpectra_0.16-2          ggcorrplot_0.1.4.1       later_1.4.2              viridisLite_0.4.2        tibble_3.2.1            
[201] memoise_2.0.1            beeswarm_0.4.0           writexl_1.5.4            cluster_2.1.8.1          HGNChelper_0.8.15       
[206] timechange_0.3.0         Stringendo_0.7.0         globals_0.18.0