hpliner
commented
4 years ago Hello, you're following the instructions for cicero for monocle3, but you have monocle2 installed. You either need to reinstall using the installation instructions for monocle3, or use the instructions for monocle2 found here
I run cicero followed the instruction, and end up with the error "could not find function "detect_genes"" when I run the code input_cds <- detect_genes(input_cds) and it seems that I've already installed cicero successfully, the sessionInfo is attached. Any suggestions would be appreciated! Thanks. Best, Ying
R version 3.6.1 (2019-07-05) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 LTS
Matrix products: default BLAS/LAPACK: /home/luh/.conda/envs/scran/lib/R/lib/libRblas.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] grid splines stats4 parallel stats graphics grDevices [8] utils datasets methods base
other attached packages: [1] cicero_1.4.4 Gviz_1.30.3 GenomicRanges_1.38.0 [4] GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4 [7] monocle_2.14.0 DDRTree_0.1.5 irlba_2.3.3 [10] VGAM_1.1-3 ggplot2_3.3.1 Biobase_2.46.0 [13] BiocGenerics_0.32.0 Matrix_1.2-18
loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_1.4-1 [3] ellipsis_0.3.0 biovizBase_1.34.1 [5] htmlTable_1.13.3 XVector_0.26.0 [7] base64enc_0.1-3 dichromat_2.0-0 [9] rstudioapi_0.11 ggrepel_0.8.2 [11] bit64_0.9-7 AnnotationDbi_1.48.0 [13] docopt_0.6.1 knitr_1.28 [15] Formula_1.2-3 Rsamtools_2.2.3 [17] cluster_2.1.0 dbplyr_1.4.3 [19] png_0.1-7 pheatmap_1.0.12 [21] compiler_3.6.1 httr_1.4.1 [23] backports_1.1.6 lazyeval_0.2.2 [25] assertthat_0.2.1 limma_3.42.2 [27] acepack_1.4.1 htmltools_0.4.0 [29] prettyunits_1.1.1 tools_3.6.1 [31] igraph_1.2.5 gtable_0.3.0 [33] glue_1.4.0 GenomeInfoDbData_1.2.2 [35] RANN_2.6.1 reshape2_1.4.4 [37] dplyr_0.8.5 rappdirs_0.3.1 [39] Rcpp_1.0.4.6 slam_0.1-47 [41] vctrs_0.3.1 Biostrings_2.54.0 [43] rtracklayer_1.46.0 xfun_0.14 [45] stringr_1.4.0 lifecycle_0.2.0 [47] ensembldb_2.10.2 XML_3.99-0.3 [49] zlibbioc_1.32.0 scales_1.1.0 [51] BSgenome_1.54.0 VariantAnnotation_1.32.0 [53] ProtGenerics_1.18.0 hms_0.5.3 [55] SummarizedExperiment_1.16.1 AnnotationFilter_1.10.0 [57] RColorBrewer_1.1-2 curl_3.3 [59] memoise_1.1.0 gridExtra_2.3 [61] biomaRt_2.42.1 rpart_4.1-15 [63] fastICA_1.2-2 latticeExtra_0.6-29 [65] stringi_1.4.6 RSQLite_2.2.0 [67] checkmate_2.0.0 GenomicFeatures_1.38.2 [69] densityClust_0.3 BiocParallel_1.22.0 [71] rlang_0.4.6 pkgconfig_2.0.3 [73] matrixStats_0.56.0 bitops_1.0-6 [75] qlcMatrix_0.9.7 lattice_0.20-41 [77] purrr_0.3.4 GenomicAlignments_1.22.1 [79] htmlwidgets_1.5.1 bit_1.1-15.2 [81] tidyselect_1.1.0 plyr_1.8.6 [83] magrittr_1.5 R6_2.4.1 [85] Hmisc_4.4-0 combinat_0.0-8 [87] DelayedArray_0.12.3 DBI_1.1.0 [89] pillar_1.4.4 foreign_0.8-71 [91] withr_2.2.0 survival_3.1-12 [93] RCurl_1.98-1.2 nnet_7.3-14 [95] tibble_3.0.1 crayon_1.3.4 [97] BiocFileCache_1.10.0 viridis_0.5.1 [99] jpeg_0.1-8.1 progress_1.2.2 [101] data.table_1.12.8 blob_1.2.1 [103] FNN_1.1.3 HSMMSingleCell_1.6.0 [105] sparsesvd_0.2 digest_0.6.25 [107] openssl_1.4.1 munsell_0.5.0 [109] viridisLite_0.3.0 askpass_1.1