Error in colnames<-(*tmp*, value = cnv_regions) : attempt to set 'colnames' on an object with less than two dimensions Calls: <Anonymous> ... <Anonymous> -> removeCNV -> removeCNV -> colnames<- Execution halted
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I ran a batch of samples and encountered this error for only one sample at step 18. Does anyone can help with this? Thank you very very much! the details is below,
Attaching SeuratObject
Attaching sp
Warning message:
package ‘Seurat’ was built under R version 4.0.5
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Loading required package: viridisLite
Warning message:
package ‘viridisLite’ was built under R version 4.0.5
Warning message:
package ‘readxl’ was built under R version 4.0.5
Warning message:
package ‘ggsci’ was built under R version 4.0.5
Attaching package: ‘cowplot’
The following object is masked from ‘package:patchwork’:
Attaching package: ‘data.table’
The following objects are masked from ‘package:dplyr’:
Warning message:
package ‘data.table’ was built under R version 4.0.5
Warning messages:
1: multiple methods tables found for ‘aperm’
2: replacing previous import ‘BiocGenerics::aperm’ by ‘DelayedArray::aperm’ when loading ‘SummarizedExperiment’
Attaching package: ‘future’
The following object is masked from ‘package:infercnv’:
Warning message:
package ‘future’ was built under R version 4.0.5
multicore:
args: function (..., workers = 20, envir = parent.frame())
tweaked: TRUE
call: plan("multicore", workers = 20)
Genome matrix has multiple modalities, returning a list of matrices for this genome
Genome matrix has multiple modalities, returning a list of matrices for this genome
INFO [2024-09-14 13:17:07] Parsing gene order file: gene_annotation.txt
INFO [2024-09-14 13:17:07] Parsing cell annotations file: cell_annotation.txt
INFO [2024-09-14 13:17:07] ::order_reduce:Start.
INFO [2024-09-14 13:17:08] .order_reduce(): expr and order match.
INFO [2024-09-14 13:17:09] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 18053,14940 Total=119590552 Min=0 Max=1580.
INFO [2024-09-14 13:17:09] num genes removed taking into account provided gene ordering list: 738 = 4.08796321940952% removed.
INFO [2024-09-14 13:17:09] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2024-09-14 13:17:12] validating infercnv_obj
INFO [2024-09-14 13:17:12] ::process_data:Start
INFO [2024-09-14 13:17:12] Creating output path output_dir
INFO [2024-09-14 13:17:12] Checking for saved results.
INFO [2024-09-14 13:17:12]
STEP 1: incoming data
INFO [2024-09-14 13:18:11]
INFO [2024-09-14 13:18:11] ::above_min_mean_expr_cutoff:Start
INFO [2024-09-14 13:18:12] Removing 7054 genes from matrix as below mean expr threshold: 0.1
INFO [2024-09-14 13:18:13] validating infercnv_obj
INFO [2024-09-14 13:18:13] There are 10261 genes and 14940 cells remaining in the expr matrix.
INFO [2024-09-14 13:18:19] no genes removed due to min cells/gene filter
INFO [2024-09-14 13:19:17]
INFO [2024-09-14 13:19:17] normalizing counts matrix by depth
INFO [2024-09-14 13:19:25] Computed total sum normalization factor as median libsize: 5699.000000
INFO [2024-09-14 13:19:25] Adding h-spike
INFO [2024-09-14 13:19:25] -hspike modeling of Normal
INFO [2024-09-14 13:20:51] validating infercnv_obj
INFO [2024-09-14 13:20:51] normalizing counts matrix by depth
INFO [2024-09-14 13:20:51] Using specified normalization factor: 5699.000000
INFO [2024-09-14 13:21:49]
INFO [2024-09-14 13:21:49] transforming log2xplus1()
INFO [2024-09-14 13:21:54] -mirroring for hspike
INFO [2024-09-14 13:21:54] transforming log2xplus1()
INFO [2024-09-14 13:22:49]
INFO [2024-09-14 13:22:49] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-09-14 13:22:49] subtracting mean(normal) per gene per cell across all data
INFO [2024-09-14 13:22:56] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-09-14 14:08:04] -mirroring for hspike
INFO [2024-09-14 14:08:04] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-09-14 14:08:04] subtracting mean(normal) per gene per cell across all data
INFO [2024-09-14 14:08:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-09-14 14:09:24]
INFO [2024-09-14 14:09:24] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2024-09-14 14:09:26] -mirroring for hspike
INFO [2024-09-14 14:09:26] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2024-09-14 14:10:44]
INFO [2024-09-14 14:10:44] smooth_by_chromosome: chr: chr1
INFO [2024-09-14 14:11:00] smooth_by_chromosome: chr: chr2
INFO [2024-09-14 14:11:13] smooth_by_chromosome: chr: chr3
INFO [2024-09-14 14:11:26] smooth_by_chromosome: chr: chr4
INFO [2024-09-14 14:11:37] smooth_by_chromosome: chr: chr5
INFO [2024-09-14 14:11:48] smooth_by_chromosome: chr: chr6
INFO [2024-09-14 14:12:00] smooth_by_chromosome: chr: chr7
INFO [2024-09-14 14:12:12] smooth_by_chromosome: chr: chr8
INFO [2024-09-14 14:12:23] smooth_by_chromosome: chr: chr9
INFO [2024-09-14 14:12:34] smooth_by_chromosome: chr: chr10
INFO [2024-09-14 14:12:45] smooth_by_chromosome: chr: chr11
INFO [2024-09-14 14:12:57] smooth_by_chromosome: chr: chr12
INFO [2024-09-14 14:13:09] smooth_by_chromosome: chr: chr13
INFO [2024-09-14 14:13:19] smooth_by_chromosome: chr: chr14
INFO [2024-09-14 14:13:29] smooth_by_chromosome: chr: chr15
INFO [2024-09-14 14:13:40] smooth_by_chromosome: chr: chr16
INFO [2024-09-14 14:13:51] smooth_by_chromosome: chr: chr17
INFO [2024-09-14 14:14:04] smooth_by_chromosome: chr: chr18
INFO [2024-09-14 14:14:13] smooth_by_chromosome: chr: chr19
INFO [2024-09-14 14:14:26] smooth_by_chromosome: chr: chr20
INFO [2024-09-14 14:14:36] smooth_by_chromosome: chr: chr21
INFO [2024-09-14 14:14:44] smooth_by_chromosome: chr: chr22
INFO [2024-09-14 14:14:54] -mirroring for hspike
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chrA
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chr_0
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chr_B
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chr_0pt5
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chr_C
INFO [2024-09-14 14:14:54] smooth_by_chromosome: chr: chr_1pt5
INFO [2024-09-14 14:14:55] smooth_by_chromosome: chr: chr_D
INFO [2024-09-14 14:14:55] smooth_by_chromosome: chr: chr_2pt0
INFO [2024-09-14 14:14:55] smooth_by_chromosome: chr: chr_E
INFO [2024-09-14 14:14:55] smooth_by_chromosome: chr: chr_3pt0
INFO [2024-09-14 14:14:55] smooth_by_chromosome: chr: chr_F
INFO [2024-09-14 14:16:15]
INFO [2024-09-14 14:16:15] ::center_smooth across chromosomes per cell
INFO [2024-09-14 14:16:34] -mirroring for hspike
INFO [2024-09-14 14:16:34] ::center_smooth across chromosomes per cell
INFO [2024-09-14 14:17:56]
INFO [2024-09-14 14:17:56] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-09-14 14:17:56] subtracting mean(normal) per gene per cell across all data
INFO [2024-09-14 14:18:02] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-09-14 14:18:11] -mirroring for hspike
INFO [2024-09-14 14:18:11] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2024-09-14 14:18:11] subtracting mean(normal) per gene per cell across all data
INFO [2024-09-14 14:18:13] -subtracting expr per gene, use_bounds=TRUE
INFO [2024-09-14 14:19:32]
INFO [2024-09-14 14:19:32] invert_log2(), computing 2^x
INFO [2024-09-14 14:19:39] -mirroring for hspike
INFO [2024-09-14 14:19:39] invert_log2(), computing 2^x
INFO [2024-09-14 14:21:18]
INFO [2024-09-14 14:21:18] define_signif_tumor_subclusters(p_val=0.1
INFO [2024-09-14 14:21:18] define_signif_tumor_subclusters(), tumor: nonNormal
INFO [2024-09-14 16:34:41] cut tree into: 1 groups
INFO [2024-09-14 16:34:41] -processing nonNormal,nonNormal_s1
INFO [2024-09-14 16:34:41] define_signif_tumor_subclusters(), tumor: Normal
INFO [2024-09-14 17:07:28] cut tree into: 1 groups
INFO [2024-09-14 17:07:28] -processing Normal,Normal_s1
INFO [2024-09-14 17:07:28] -mirroring for hspike
INFO [2024-09-14 17:07:28] define_signif_tumor_subclusters(p_val=0.1
INFO [2024-09-14 17:07:28] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_Normal
INFO [2024-09-14 17:07:29] cut tree into: 1 groups
INFO [2024-09-14 17:07:29] -processing spike_tumor_cell_Normal,spike_tumor_cell_Normal_s1
INFO [2024-09-14 17:07:29] define_signif_tumor_subclusters(), tumor: simnorm_cell_Normal
INFO [2024-09-14 17:07:29] cut tree into: 1 groups
INFO [2024-09-14 17:07:29] -processing simnorm_cell_Normal,simnorm_cell_Normal_s1
INFO [2024-09-14 17:10:54] ::plot_cnv:Start
INFO [2024-09-14 17:10:54] ::plot_cnv:Current data dimensions (r,c)=10261,14940 Total=153509246.09245 Min=0.748074948144627 Max=1.76922508407909.
INFO [2024-09-14 17:10:56] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2024-09-14 17:13:18] plot_cnv(): auto thresholding at: (0.852785 , 1.149953)
INFO [2024-09-14 17:13:21] plot_cnv_observation:Start
INFO [2024-09-14 17:13:21] Observation data size: Cells= 9759 Genes= 10261
INFO [2024-09-14 17:13:22] plot_cnv_observation:Writing observation groupings/color.
INFO [2024-09-14 17:13:23] plot_cnv_observation:Done writing observation groupings/color.
INFO [2024-09-14 17:13:23] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2024-09-14 17:13:23] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2024-09-14 17:13:39] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 17:13:39] Quantiles of plotted data range: 0.852785416553159,0.967036120978011,0.997480470597608,1.03055510080462,1.14995309611689
INFO [2024-09-14 17:13:53] plot_cnv_observations:Writing observation data to output_dir/infercnv.preliminary.observations.txt
INFO [2024-09-14 17:15:20] plot_cnv_references:Start
INFO [2024-09-14 17:15:20] Reference data size: Cells= 5181 Genes= 10261
INFO [2024-09-14 17:47:05] plot_cnv_references:Number reference groups= 1
INFO [2024-09-14 17:47:06] plot_cnv_references:Plotting heatmap.
INFO [2024-09-14 17:47:13] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 17:47:13] Quantiles of plotted data range: 0.852785416553159,0.961829157004469,0.997480448133121,1.03683235661565,1.14995309611689
INFO [2024-09-14 17:47:18] plot_cnv_references:Writing reference data to output_dir/infercnv.preliminary.references.txt
INFO [2024-09-14 17:48:04]
INFO [2024-09-14 17:48:04] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2024-09-14 17:48:06] -done predicting CNV based on initial tumor subclusters
INFO [2024-09-14 17:48:44] get_predicted_CNV_regions(subcluster)
INFO [2024-09-14 17:48:44] -processing cell_group_name: nonNormal.nonNormal_s1, size: 9759
INFO [2024-09-14 17:49:53] -processing cell_group_name: Normal.Normal_s1, size: 5181
INFO [2024-09-14 17:50:31] -writing cell clusters file: output_dir/17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2024-09-14 17:50:31] -writing cnv regions file: output_dir/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2024-09-14 17:50:31] -writing per-gene cnv report: output_dir/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2024-09-14 17:50:31] -writing gene ordering info: output_dir/17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2024-09-14 17:50:32] ::plot_cnv:Start
INFO [2024-09-14 17:50:32] ::plot_cnv:Current data dimensions (r,c)=10261,14940 Total=461654640 Min=3 Max=4.
INFO [2024-09-14 17:50:33] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2024-09-14 17:52:27] plot_cnv_observation:Start
INFO [2024-09-14 17:52:27] Observation data size: Cells= 9759 Genes= 10261
INFO [2024-09-14 17:52:28] plot_cnv_observation:Writing observation groupings/color.
INFO [2024-09-14 17:52:28] plot_cnv_observation:Done writing observation groupings/color.
INFO [2024-09-14 17:52:29] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2024-09-14 17:52:29] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2024-09-14 17:52:43] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 17:52:43] Quantiles of plotted data range: 3,3,3,3,4
INFO [2024-09-14 17:52:53] plot_cnv_observations:Writing observation data to output_dir/infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2024-09-14 17:54:07] plot_cnv_references:Start
INFO [2024-09-14 17:54:07] Reference data size: Cells= 5181 Genes= 10261
INFO [2024-09-14 18:26:40] plot_cnv_references:Number reference groups= 1
INFO [2024-09-14 18:26:40] plot_cnv_references:Plotting heatmap.
INFO [2024-09-14 18:26:47] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 18:26:47] Quantiles of plotted data range: 3,3,3,3,3
INFO [2024-09-14 18:26:51] plot_cnv_references:Writing reference data to output_dir/infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2024-09-14 18:27:34]
INFO [2024-09-14 18:27:34] Creating the following Directory: output_dir/BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2024-09-14 18:27:34] Initializing new MCM InferCNV Object.
INFO [2024-09-14 18:27:34] validating infercnv_obj
INFO [2024-09-14 18:27:35] Total CNV's: 2
INFO [2024-09-14 18:27:35] Loading BUGS Model.
INFO [2024-09-14 18:27:35] Running Sampling Using Parallel with 4 Cores
INFO [2024-09-14 19:01:19] Obtaining probabilities post-sampling
INFO [2024-09-14 19:02:32] Gibbs sampling time: 34.9505852103233 Minutes
INFO [2024-09-14 19:04:12] ::plot_cnv:Start
INFO [2024-09-14 19:04:12] ::plot_cnv:Current data dimensions (r,c)=10261,14940 Total=891975.312791351 Min=0 Max=0.579024400712812.
INFO [2024-09-14 19:04:14] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2024-09-14 19:04:17] plot_cnv_observation:Start
INFO [2024-09-14 19:04:17] Observation data size: Cells= 9759 Genes= 10261
INFO [2024-09-14 19:04:18] plot_cnv_observation:Writing observation groupings/color.
INFO [2024-09-14 19:04:18] plot_cnv_observation:Done writing observation groupings/color.
INFO [2024-09-14 19:04:18] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2024-09-14 19:04:18] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2024-09-14 19:04:32] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 19:04:32] Quantiles of plotted data range: 0,0,0,0,0.579024400712812
INFO [2024-09-14 19:04:42] plot_cnv_observations:Writing observation data to output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2024-09-14 19:05:37] plot_cnv_references:Start
INFO [2024-09-14 19:05:37] Reference data size: Cells= 5181 Genes= 10261
INFO [2024-09-14 19:42:31] plot_cnv_references:Number reference groups= 1
INFO [2024-09-14 19:42:31] plot_cnv_references:Plotting heatmap.
INFO [2024-09-14 19:42:39] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2024-09-14 19:42:39] Quantiles of plotted data range: 0,0,0,0,0
INFO [2024-09-14 19:42:42] plot_cnv_references:Writing reference data to output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2024-09-14 19:44:52] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2024-09-14 19:44:52] Removing 1 CNV(s) identified by the HMM.
INFO [2024-09-14 19:44:52] Total CNV's after removing: 1
Error in
colnames<-(*tmp*, value = cnv_regions) :attempt to set 'colnames' on an object with less than two dimensions
Calls: ... -> removeCNV -> removeCNV -> colnames<-
Execution halted
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.7 (Ootpa)
Matrix products: default
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
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] infercnv_1.6.0 data.table_1.14.2 cowplot_1.1.3
[4] ggsci_2.9 readxl_1.4.1 viridis_0.6.5
[7] viridisLite_0.4.1 dplyr_1.1.4 patchwork_1.2.0.9000
[10] ggplot2_3.5.1 sp_1.5-0 SeuratObject_4.1.1
[13] Seurat_4.1.1
loaded via a namespace (and not attached):
[1] plyr_1.8.7 igraph_2.0.3
[3] lazyeval_0.2.2 splines_4.0.3
[5] listenv_0.8.0 scattermore_0.8
[7] TH.data_1.1-2 GenomeInfoDb_1.26.4
[9] digest_0.6.36 foreach_1.5.2
[11] htmltools_0.5.8.1 fansi_1.0.3
[13] magrittr_2.0.3 tensor_1.5
[15] cluster_2.1.3 doParallel_1.0.17
[17] ROCR_1.0-11 limma_3.46.0
[19] fastcluster_1.2.6 globals_0.16.1
[21] matrixStats_0.62.0 sandwich_3.1-0
[23] spatstat.sparse_3.1-0 colorspace_2.0-3
[25] ggrepel_0.9.5 libcoin_1.0-10
[27] RCurl_1.98-1.3 jsonlite_1.8.8
[29] progressr_0.11.0 spatstat.data_3.1-2
[31] survival_3.4-0 zoo_1.8-11
[33] iterators_1.0.14 ape_5.8
[35] glue_1.6.2 polyclip_1.10-0
[37] gtable_0.3.1 zlibbioc_1.36.0
[39] XVector_0.30.0 leiden_0.4.3
[41] DelayedArray_0.16.3 future.apply_1.9.1
[43] SingleCellExperiment_1.12.0 BiocGenerics_0.50.0
[45] abind_1.4-5 scales_1.3.0
[47] mvtnorm_1.2-5 futile.options_1.0.1
[49] edgeR_4.2.0 miniUI_0.1.1.1
[51] Rcpp_1.0.9 xtable_1.8-4
[53] reticulate_1.30 spatstat.core_2.3-2
[55] stats4_4.0.3 htmlwidgets_1.5.4
[57] httr_1.4.7 gplots_3.1.3
[59] RColorBrewer_1.1-3 modeltools_0.2-23
[61] ica_1.0-3 reshape_0.8.9
[63] pkgconfig_2.0.3 uwot_0.1.14
[65] deldir_1.0-6 locfit_1.5-9.4
[67] utf8_1.2.2 tidyselect_1.2.1
[69] rlang_1.1.4 reshape2_1.4.4
[71] later_1.2.0 munsell_0.5.0
[73] cellranger_1.1.0 tools_4.0.3
[75] cli_3.6.3 generics_0.1.3
[77] ggridges_0.5.4 stringr_1.5.1
[79] fastmap_1.2.0 argparse_2.2.3
[81] goftest_1.2-3 fitdistrplus_1.1-8
[83] caTools_1.18.2 purrr_1.0.2
[85] RANN_2.6.1 coin_1.4-3
[87] pbapply_1.5-0 future_1.28.0
[89] nlme_3.1-159 mime_0.12
[91] formatR_1.12 compiler_4.0.3
[93] plotly_4.10.0 png_0.1-7
[95] spatstat.utils_3.0-5 tibble_3.2.1
[97] stringi_1.7.6 futile.logger_1.4.3
[99] rgeos_0.5-8 lattice_0.20-45
[101] Matrix_1.4-1 vctrs_0.6.5
[103] pillar_1.9.0 lifecycle_1.0.4
[105] spatstat.geom_3.2-9 lmtest_0.9-40
[107] RcppAnnoy_0.0.19 bitops_1.0-7
[109] irlba_2.3.5 httpuv_1.6.6
[111] GenomicRanges_1.42.0 R6_2.5.1
[113] promises_1.2.0.1 KernSmooth_2.23-20
[115] gridExtra_2.3 rjags_4-15
[117] IRanges_2.24.1 parallelly_1.32.1
[119] codetools_0.2-18 lambda.r_1.2.4
[121] gtools_3.9.3 MASS_7.3-58.1
[123] SummarizedExperiment_1.20.0 withr_2.5.0
[125] sctransform_0.3.4 multcomp_1.4-25
[127] S4Vectors_0.28.1 GenomeInfoDbData_1.2.4
[129] mgcv_1.8-40 parallel_4.0.3
[131] grid_4.0.3 rpart_4.1.16
[133] tidyr_1.3.1 coda_0.19-4.1
[135] MatrixGenerics_1.2.1 Rtsne_0.16
[137] Biobase_2.50.0 shiny_1.9.1
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