Getting error while computing footprint for a manually supplied set of peaks as a list.

[raunakkar]

Hi, I am trying to get footprint data for a set of TFs in a given set of peaks from my dataset. But I am getting the error "Error in fixupDN.if.valid(value, x@Dim): length of Dimnames[[1]] (4096) is not equal to Dim[1] (4093)".

Could you please guide me as to what could be the problem?

Thanks in advance!

[raunakkar]

As a prologue to what I am trying to do, I am attaching the region of the code I am trying to run:

overlap_peaks <- findOverlaps(combined2, StringToGRanges("chr2-85680000-85710000"))
granges(combined2)[queryHits(overlap_peaks)] -> peaks.of.interest

instances <- matchMotifs(pfm2, peaks.of.interest genome = "hg38", out="positions")
combined2 <- Footprint(
  object = combined2,
  key = c("TBX21_MA0690.1", "EOMES_MA0800.1"),
  assay = 'peaks',
  in.peaks = TRUE,
  genome = BSgenome.Hsapiens.UCSC.hg38,
  regions = list(instances[["TBX21_MA0690.1"]], instances[["EOMES_MA0800.1"]])
)

[raunakkar]

Sorry for writing this multiple comments. But I wanted to add that the above code is running find if I provide "compute.expected = FALSE" while running Footprint. However in that case I cannot get the relevant data in the object. GetFootprintData(combined2, features = c("TBX21_MA0690.1"), group.by = "wsnn_res.0.4", assay = "peaks")

Warning message in FUN(X[[i]], ...):
"Footprint information for TBX21_MA0690.1 not found in assay"

[timoast]

Hi @raunakkar, please show the full code and output of sessionInfo()

[raunakkar]

Hi @timoast, Please find below the full code I wa trying to run:

combined2

An object of class Seurat 260102 features across 30946 samples within 4 assays Active assay: peaks (100647 features, 100646 variable features) 2 layers present: counts, data 3 other assays present: ATAC, RNA, SCT 6 dimensional reductions calculated: lsi, umap, pca, wnn.umap, umap.rna, umap.atac

main.chroms <- standardChromosomes(BSgenome.Hsapiens.UCSC.hg38)
keep.peaks <- as.logical(seqnames(granges(combined2)) %in% main.chroms)
combined2[["peaks"]] <- subset(combined2[["peaks"]], features = rownames(combined2[["peaks"]])[keep.peaks])

pfm2 <- readJASPARMatrix(
        "/home/igl/CellRangerReferences/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/regions/motifs.pfm", 
        matrixClass="PFM")

add motif information

combined2 <- AddMotifs(
  object = combined2,
  genome = BSgenome.Hsapiens.UCSC.hg38,
  pfm = pfm2
)

combined2[["peaks"]]

ChromatinAssay data with 100647 features for 30946 cells Variable features: 100646 Genome: Annotation present: TRUE Motifs present: TRUE Fragment files: 4

overlap_peaks <- findOverlaps(combined2, StringToGRanges("chr2-85680000-85710000"))
granges(combined2)[queryHits(overlap_peaks)] -> peaks.of.interest

instances <- matchMotifs(pfm2, peaks.of.interest, genome = "hg38", out="positions")

combined2 <- Footprint(
  object = combined2,
  key = c("TBX21_MA0690.1", "EOMES_MA0800.1"),
  assay = 'peaks',
  in.peaks = TRUE,
  genome = BSgenome.Hsapiens.UCSC.hg38,
  regions = list(instances[["TBX21_MA0690.1"]], instances[["EOMES_MA0800.1"]])
)`

This is where the following error pops up:

Computing Tn5 insertion bias

Extracting reads in requested region

Extracting reads in requested region

Extracting reads in requested region

Extracting reads in requested region

Computing observed Tn5 insertions per base

Computing base composition at motif sites

Error in fixupDN.if.valid(value, x@Dim): length of Dimnames[[1]] (4096) is not equal to Dim[1] (4093)

In the last step, upon trying "compute.expected = FALSE", the Footprinting runs fine, but the following problem pops up:

PlotFootprint(combined2, features = c("TBX21_MA0690.1"), 
              #group.by = "wsnn_res.0.4", 
              assay = "peaks")

Warning message in FUN(X[[i]], ...): "Footprint information for TBX21_MA0690.1 not found in assay"

Error in PlotFootprint(combined2, features = c("TBX21_MA0690.1"), assay = "peaks"): Footprinting data not found Traceback:

1. PlotFootprint(combined2, features = c("TBX21_MA0690.1"), assay = "peaks")
2. stop("Footprinting data not found")

Please find below the output for sessionInfo()

R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: AlmaLinux 9.3 (Shamrock Pampas Cat)

Matrix products: default BLAS/LAPACK: /home/igl/mambaforge/lib/libopenblasp-r0.3.23.so

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] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] biovizBase_1.46.0
[2] harmony_0.1.1
[3] scales_1.3.0
[4] biomaRt_2.54.1
[5] sctransform_0.4.1
[6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0 [7] ChIPseeker_1.34.1
[8] BSgenome.Hsapiens.UCSC.hg38_1.4.5
[9] BSgenome_1.66.3
[10] rtracklayer_1.58.0
[11] Biostrings_2.66.0
[12] XVector_0.38.0
[13] JASPAR2022_0.99.7
[14] BiocFileCache_2.6.1
[15] dbplyr_2.3.3
[16] presto_1.0.0
[17] data.table_1.14.10
[18] Rcpp_1.0.11
[19] motifmatchr_1.20.0
[20] TFBSTools_1.36.0
[21] chromVAR_1.20.2
[22] pheatmap_1.0.12
[23] MAST_1.24.1
[24] SingleCellExperiment_1.20.0
[25] SummarizedExperiment_1.28.0
[26] MatrixGenerics_1.10.0
[27] matrixStats_1.2.0
[28] ggalluvial_0.12.5
[29] Nebulosa_1.8.0
[30] clustree_0.5.0
[31] ggraph_2.1.0
[32] ggpubr_0.6.0
[33] qs_0.25.5
[34] scCustomize_1.1.1
[35] viridis_0.6.4
[36] viridisLite_0.4.2
[37] lubridate_1.9.2
[38] forcats_1.0.0
[39] stringr_1.5.1
[40] purrr_1.0.2
[41] readr_2.1.4
[42] tidyr_1.3.0
[43] tibble_3.2.1
[44] tidyverse_2.0.0
[45] igraph_1.6.0
[46] dplyr_1.1.4
[47] patchwork_1.1.3
[48] ggplot2_3.4.4
[49] EnsDb.Hsapiens.v86_2.99.0
[50] ensembldb_2.22.0
[51] AnnotationFilter_1.22.0
[52] GenomicFeatures_1.50.4
[53] AnnotationDbi_1.60.2
[54] Biobase_2.58.0
[55] future_1.33.1
[56] GenomicRanges_1.50.2
[57] GenomeInfoDb_1.34.9
[58] IRanges_2.32.0
[59] S4Vectors_0.36.2
[60] BiocGenerics_0.44.0
[61] Seurat_5.0.1
[62] SeuratObject_5.0.1
[63] sp_2.1-2
[64] Signac_1.10.0

loaded via a namespace (and not attached): [1] Hmisc_5.1-0
[2] ica_1.0-3
[3] RcppRoll_0.3.0
[4] Rsamtools_2.14.0
[5] lmtest_0.9-40
[6] crayon_1.5.2
[7] MASS_7.3-60
[8] nlme_3.1-164
[9] backports_1.4.1
[10] GOSemSim_2.24.0
[11] rlang_1.1.2
[12] HDO.db_0.99.1
[13] ROCR_1.0-11
[14] irlba_2.3.5.1
[15] filelock_1.0.2
[16] stringfish_0.15.8
[17] BiocParallel_1.32.6
[18] rjson_0.2.21
[19] CNEr_1.34.0
[20] bit64_4.0.5
[21] glue_1.6.2
[22] poweRlaw_0.70.6
[23] parallel_4.2.2
[24] vipor_0.4.5
[25] spatstat.sparse_3.0-3
[26] dotCall64_1.1-1
[27] DOSE_3.24.2
[28] spatstat.geom_3.2-7
[29] tidyselect_1.2.0
[30] fitdistrplus_1.1-11
[31] XML_3.99-0.14
[32] zoo_1.8-12
[33] GenomicAlignments_1.34.1
[34] xtable_1.8-4
[35] RcppHNSW_0.5.0
[36] magrittr_2.0.3
[37] evaluate_0.23
[38] cli_3.6.2
[39] zlibbioc_1.44.0
[40] rstudioapi_0.15.0
[41] miniUI_0.1.1.1
[42] rpart_4.1.19
[43] fastmatch_1.1-4
[44] treeio_1.22.0
[45] fastDummies_1.7.3
[46] shiny_1.8.0
[47] xfun_0.41
[48] cluster_2.1.4
[49] caTools_1.18.2
[50] tidygraph_1.2.3
[51] pbdZMQ_0.3-9
[52] KEGGREST_1.38.0
[53] ggrepel_0.9.4
[54] ape_5.7-1
[55] listenv_0.9.0
[56] TFMPvalue_0.0.9
[57] png_0.1-8
[58] withr_2.5.2
[59] bitops_1.0-7
[60] ggforce_0.4.1
[61] plyr_1.8.9
[62] pracma_2.4.2
[63] pillar_1.9.0
[64] RcppParallel_5.1.6
[65] gplots_3.1.3
[66] GlobalOptions_0.1.2
[67] cachem_1.0.8
[68] paletteer_1.5.0
[69] vctrs_0.6.5
[70] ellipsis_0.3.2
[71] generics_0.1.3
[72] RApiSerialize_0.1.2
[73] tools_4.2.2
[74] foreign_0.8-84
[75] beeswarm_0.4.0
[76] munsell_0.5.0
[77] tweenr_2.0.2
[78] fgsea_1.24.0
[79] DelayedArray_0.24.0
[80] fastmap_1.1.1
[81] compiler_4.2.2
[82] abind_1.4-5
[83] httpuv_1.6.13
[84] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [85] plotly_4.10.3
[86] GenomeInfoDbData_1.2.9
[87] gridExtra_2.3
[88] lattice_0.21-8
[89] deldir_2.0-2
[90] utf8_1.2.4
[91] later_1.3.2
[92] jsonlite_1.8.8
[93] tidytree_0.4.4
[94] pbapply_1.7-2
[95] carData_3.0-5
[96] lazyeval_0.2.2
[97] promises_1.2.1
[98] car_3.1-2
[99] R.utils_2.12.2
[100] goftest_1.2-3
[101] checkmate_2.2.0
[102] spatstat.utils_3.0-4
[103] reticulate_1.34.0
[104] rmarkdown_2.25
[105] cowplot_1.1.2
[106] Rtsne_0.17
[107] dichromat_2.0-0.1
[108] uwot_0.1.16
[109] plotrix_3.8-2
[110] survival_3.5-5
[111] yaml_2.3.8
[112] htmltools_0.5.7
[113] memoise_2.0.1
[114] VariantAnnotation_1.44.1
[115] BiocIO_1.8.0
[116] graphlayouts_1.0.0
[117] digest_0.6.33
[118] mime_0.12
[119] rappdirs_0.3.3
[120] repr_1.1.6
[121] spam_2.10-0
[122] RSQLite_2.3.1
[123] yulab.utils_0.0.6
[124] future.apply_1.11.1
[125] blob_1.2.4
[126] R.oo_1.25.0
[127] Formula_1.2-5
[128] splines_4.2.2
[129] rematch2_2.1.2
[130] ProtGenerics_1.30.0
[131] RCurl_1.98-1.12
[132] broom_1.0.5
[133] ks_1.14.0
[134] hms_1.1.3
[135] colorspace_2.1-0
[136] base64enc_0.1-3
[137] ggbeeswarm_0.7.2
[138] shape_1.4.6
[139] aplot_0.1.10
[140] nnet_7.3-19
[141] ggrastr_1.0.2
[142] mclust_6.0.0
[143] RANN_2.6.1
[144] mvtnorm_1.2-2
[145] circlize_0.4.15
[146] enrichplot_1.18.4
[147] fansi_1.0.6
[148] tzdb_0.4.0
[149] parallelly_1.36.0
[150] IRdisplay_1.1
[151] R6_2.5.1
[152] grid_4.2.2
[153] ggridges_0.5.5
[154] lifecycle_1.0.4
[155] curl_5.2.0
[156] ggsignif_0.6.4
[157] leiden_0.4.3.1
[158] snakecase_0.11.0
[159] Matrix_1.6-4
[160] qvalue_2.30.0
[161] RcppAnnoy_0.0.21
[162] RColorBrewer_1.1-3
[163] spatstat.explore_3.2-5
[164] htmlwidgets_1.6.4
[165] polyclip_1.10-6
[166] shadowtext_0.1.2
[167] gridGraphics_0.5-1
[168] timechange_0.2.0
[169] seqLogo_1.64.0
[170] globals_0.16.2
[171] htmlTable_2.4.1
[172] spatstat.random_3.2-2
[173] progressr_0.14.0
[174] codetools_0.2-19
[175] GO.db_3.16.0
[176] gtools_3.9.5
[177] prettyunits_1.1.1
[178] RSpectra_0.16-1
[179] R.methodsS3_1.8.2
[180] gtable_0.3.4
[181] DBI_1.1.3
[182] ggfun_0.1.1
[183] tensor_1.5
[184] httr_1.4.7
[185] KernSmooth_2.23-21
[186] stringi_1.8.3
[187] progress_1.2.2
[188] reshape2_1.4.4
[189] farver_2.1.1
[190] uuid_1.1-0
[191] annotate_1.76.0
[192] ggtree_3.6.2
[193] DT_0.28
[194] xml2_1.3.5
[195] boot_1.3-28.1
[196] IRkernel_1.3.2
[197] restfulr_0.0.15
[198] ggplotify_0.1.1
[199] scattermore_1.2
[200] bit_4.0.5
[201] scatterpie_0.2.1
[202] spatstat.data_3.0-3
[203] janitor_2.2.0
[204] pkgconfig_2.0.3
[205] DirichletMultinomial_1.40.0
[206] ggprism_1.0.4
[207] rstatix_0.7.2
[208] knitr_1.45

[raunakkar]

Please let me know if anything else would be required. Thanks a lot.

[timoast]

Please update Signac to the latest version and try again:

remotes::install_github("stuart-lab/signac", ref="develop")

[raunakkar]

Hi @timoast , I tried updating Signac package, but the same problem persists. Please find attached below the new sessionInfo()

R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: AlmaLinux 9.3 (Shamrock Pampas Cat)

Matrix products: default BLAS/LAPACK: /home/igl/mambaforge/lib/libopenblasp-r0.3.23.so

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] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] biovizBase_1.46.0
[2] harmony_0.1.1
[3] scales_1.3.0
[4] biomaRt_2.54.1
[5] sctransform_0.4.1
[6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0 [7] ChIPseeker_1.34.1
[8] BSgenome.Hsapiens.UCSC.hg38_1.4.5
[9] BSgenome_1.66.3
[10] rtracklayer_1.58.0
[11] Biostrings_2.66.0
[12] XVector_0.38.0
[13] JASPAR2022_0.99.7
[14] BiocFileCache_2.6.1
[15] dbplyr_2.3.3
[16] presto_1.0.0
[17] data.table_1.15.0
[18] Rcpp_1.0.12
[19] motifmatchr_1.20.0
[20] TFBSTools_1.36.0
[21] chromVAR_1.20.2
[22] pheatmap_1.0.12
[23] MAST_1.24.1
[24] SingleCellExperiment_1.20.0
[25] SummarizedExperiment_1.28.0
[26] MatrixGenerics_1.10.0
[27] matrixStats_1.2.0
[28] ggalluvial_0.12.5
[29] Nebulosa_1.8.0
[30] clustree_0.5.0
[31] ggraph_2.1.0
[32] ggpubr_0.6.0
[33] qs_0.25.5
[34] scCustomize_1.1.1
[35] viridis_0.6.4
[36] viridisLite_0.4.2
[37] lubridate_1.9.2
[38] forcats_1.0.0
[39] stringr_1.5.1
[40] purrr_1.0.2
[41] readr_2.1.4
[42] tidyr_1.3.1
[43] tibble_3.2.1
[44] tidyverse_2.0.0
[45] igraph_1.6.0
[46] dplyr_1.1.4
[47] patchwork_1.2.0
[48] ggplot2_3.4.4
[49] EnsDb.Hsapiens.v86_2.99.0
[50] ensembldb_2.22.0
[51] AnnotationFilter_1.22.0
[52] GenomicFeatures_1.50.4
[53] AnnotationDbi_1.60.2
[54] Biobase_2.58.0
[55] future_1.33.1
[56] GenomicRanges_1.50.2
[57] GenomeInfoDb_1.34.9
[58] IRanges_2.32.0
[59] S4Vectors_0.36.2
[60] BiocGenerics_0.44.0
[61] Seurat_5.0.1
[62] SeuratObject_5.0.1
[63] sp_2.1-3
[64] Signac_1.12.9004

loaded via a namespace (and not attached): [1] Hmisc_5.1-0
[2] ica_1.0-3
[3] RcppRoll_0.3.0
[4] ps_1.7.5
[5] Rsamtools_2.14.0
[6] rprojroot_2.0.4
[7] lmtest_0.9-40
[8] crayon_1.5.2
[9] MASS_7.3-60
[10] nlme_3.1-164
[11] backports_1.4.1
[12] GOSemSim_2.24.0
[13] rlang_1.1.3
[14] HDO.db_0.99.1
[15] ROCR_1.0-11
[16] irlba_2.3.5.1
[17] callr_3.7.3
[18] filelock_1.0.2
[19] stringfish_0.15.8
[20] BiocParallel_1.32.6
[21] rjson_0.2.21
[22] CNEr_1.34.0
[23] bit64_4.0.5
[24] glue_1.7.0
[25] poweRlaw_0.70.6
[26] processx_3.8.3
[27] parallel_4.2.2
[28] vipor_0.4.5
[29] spatstat.sparse_3.0-3
[30] dotCall64_1.1-1
[31] DOSE_3.24.2
[32] spatstat.geom_3.2-7
[33] tidyselect_1.2.0
[34] fitdistrplus_1.1-11
[35] XML_3.99-0.14
[36] zoo_1.8-12
[37] GenomicAlignments_1.34.1
[38] xtable_1.8-4
[39] RcppHNSW_0.5.0
[40] magrittr_2.0.3
[41] evaluate_0.23
[42] cli_3.6.2
[43] zlibbioc_1.44.0
[44] rstudioapi_0.15.0
[45] miniUI_0.1.1.1
[46] rpart_4.1.19
[47] fastmatch_1.1-4
[48] treeio_1.22.0
[49] fastDummies_1.7.3
[50] shiny_1.8.0
[51] xfun_0.41
[52] pkgbuild_1.4.2
[53] cluster_2.1.4
[54] caTools_1.18.2
[55] tidygraph_1.2.3
[56] pbdZMQ_0.3-9
[57] KEGGREST_1.38.0
[58] ggrepel_0.9.4
[59] ape_5.7-1
[60] listenv_0.9.1
[61] TFMPvalue_0.0.9
[62] png_0.1-8
[63] withr_3.0.0
[64] bitops_1.0-7
[65] ggforce_0.4.1
[66] plyr_1.8.9
[67] pracma_2.4.2
[68] pillar_1.9.0
[69] RcppParallel_5.1.6
[70] gplots_3.1.3
[71] GlobalOptions_0.1.2
[72] cachem_1.0.8
[73] paletteer_1.5.0
[74] vctrs_0.6.5
[75] ellipsis_0.3.2
[76] generics_0.1.3
[77] RApiSerialize_0.1.2
[78] tools_4.2.2
[79] foreign_0.8-84
[80] beeswarm_0.4.0
[81] munsell_0.5.0
[82] tweenr_2.0.2
[83] fgsea_1.24.0
[84] DelayedArray_0.24.0
[85] fastmap_1.1.1
[86] compiler_4.2.2
[87] abind_1.4-5
[88] httpuv_1.6.13
[89] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [90] plotly_4.10.3
[91] GenomeInfoDbData_1.2.9
[92] gridExtra_2.3
[93] lattice_0.21-8
[94] deldir_2.0-2
[95] utf8_1.2.4
[96] later_1.3.2
[97] jsonlite_1.8.8
[98] tidytree_0.4.4
[99] pbapply_1.7-2
[100] carData_3.0-5
[101] lazyeval_0.2.2
[102] promises_1.2.1
[103] car_3.1-2
[104] R.utils_2.12.2
[105] goftest_1.2-3
[106] checkmate_2.2.0
[107] spatstat.utils_3.0-4
[108] reticulate_1.34.0
[109] rmarkdown_2.25
[110] cowplot_1.1.2
[111] Rtsne_0.17
[112] dichromat_2.0-0.1
[113] uwot_0.1.16
[114] plotrix_3.8-2
[115] survival_3.5-5
[116] yaml_2.3.8
[117] htmltools_0.5.7
[118] memoise_2.0.1
[119] VariantAnnotation_1.44.1
[120] BiocIO_1.8.0
[121] graphlayouts_1.0.0
[122] digest_0.6.34
[123] mime_0.12
[124] rappdirs_0.3.3
[125] repr_1.1.6
[126] spam_2.10-0
[127] RSQLite_2.3.1
[128] yulab.utils_0.0.6
[129] future.apply_1.11.1
[130] remotes_2.4.2.1
[131] blob_1.2.4
[132] R.oo_1.25.0
[133] Formula_1.2-5
[134] splines_4.2.2
[135] rematch2_2.1.2
[136] ProtGenerics_1.30.0
[137] RCurl_1.98-1.12
[138] broom_1.0.5
[139] ks_1.14.0
[140] hms_1.1.3
[141] colorspace_2.1-0
[142] base64enc_0.1-3
[143] ggbeeswarm_0.7.2
[144] shape_1.4.6
[145] aplot_0.1.10
[146] nnet_7.3-19
[147] ggrastr_1.0.2
[148] mclust_6.0.0
[149] RANN_2.6.1
[150] mvtnorm_1.2-2
[151] circlize_0.4.15
[152] enrichplot_1.18.4
[153] fansi_1.0.6
[154] tzdb_0.4.0
[155] parallelly_1.36.0
[156] IRdisplay_1.1
[157] R6_2.5.1
[158] grid_4.2.2
[159] ggridges_0.5.5
[160] lifecycle_1.0.4
[161] curl_5.2.0
[162] ggsignif_0.6.4
[163] leiden_0.4.3.1
[164] snakecase_0.11.0
[165] Matrix_1.6-4
[166] qvalue_2.30.0
[167] desc_1.4.3
[168] RcppAnnoy_0.0.21
[169] RColorBrewer_1.1-3
[170] spatstat.explore_3.2-5
[171] htmlwidgets_1.6.4
[172] polyclip_1.10-6
[173] shadowtext_0.1.2
[174] gridGraphics_0.5-1
[175] timechange_0.2.0
[176] seqLogo_1.64.0
[177] globals_0.16.2
[178] htmlTable_2.4.1
[179] spatstat.random_3.2-2
[180] progressr_0.14.0
[181] codetools_0.2-19
[182] GO.db_3.16.0
[183] gtools_3.9.5
[184] prettyunits_1.1.1
[185] RSpectra_0.16-1
[186] R.methodsS3_1.8.2
[187] gtable_0.3.4
[188] DBI_1.1.3
[189] ggfun_0.1.1
[190] tensor_1.5
[191] httr_1.4.7
[192] KernSmooth_2.23-21
[193] stringi_1.8.3
[194] progress_1.2.2
[195] reshape2_1.4.4
[196] farver_2.1.1
[197] uuid_1.1-0
[198] annotate_1.76.0
[199] ggtree_3.6.2
[200] DT_0.28
[201] xml2_1.3.5
[202] boot_1.3-28.1
[203] IRkernel_1.3.2
[204] restfulr_0.0.15
[205] ggplotify_0.1.1
[206] scattermore_1.2
[207] bit_4.0.5
[208] scatterpie_0.2.1
[209] spatstat.data_3.0-3
[210] janitor_2.2.0
[211] pkgconfig_2.0.3
[212] DirichletMultinomial_1.40.0
[213] ggprism_1.0.4
[214] rstatix_0.7.2
[215] knitr_1.45

[timoast]

Hi @raunakkar, sorry for the delay. This should now be fixed on the develop branch, please install from develop and check if you still have the error:

remotes::install_github("stuart-lab/signac", ref = "develop")