Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
Hi Beate,
it powsimR seems to be a very useful tool, thanks for developing it. I was able to install it in my machine but I keep receiving an error when I try to reproduce your example. See below. Do you have any hints on what may be causing it?
thanks,
Fernando
Hi Beate, it powsimR seems to be a very useful tool, thanks for developing it. I was able to install it in my machine but I keep receiving an error when I try to reproduce your example. See below. Do you have any hints on what may be causing it? thanks, Fernando
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] scater_1.8.0 ggplot2_2.2.1 powsimR_1.1.1 gamlss.dist_5.0-6 MASS_7.3-50 SingleCellExperiment_1.2.0 [7] SummarizedExperiment_1.10.1 DelayedArray_0.6.0 BiocParallel_1.14.1 matrixStats_0.53.1 Biobase_2.40.0 GenomicRanges_1.32.3
[13] GenomeInfoDb_1.16.0 IRanges_2.14.10 S4Vectors_0.18.3 BiocGenerics_0.26.0
loaded via a namespace (and not attached): [1] mixtools_1.1.0 softImpute_1.4 minpack.lm_1.2-1 pbapply_1.3-4 haven_1.1.1 lattice_0.20-35 fastICA_1.2-1
[8] mgcv_1.8-23 penalized_0.9-50 blob_1.1.1 survival_2.42-3 prodlim_2018.04.18 later_0.7.3 nloptr_1.0.4
[15] DBI_1.0.0 R.utils_2.6.0 Linnorm_2.4.0 bindr_0.1.1 zlibbioc_1.26.0 MatrixModels_0.4-1 pspline_1.0-18
[22] pcaMethods_1.72.0 SDMTools_1.1-221 htmlwidgets_1.2 mvtnorm_1.0-8 UpSetR_1.3.3 tclust_1.4-1 irlba_2.3.2
[29] DEoptimR_1.0-8 lars_1.2 Rcpp_0.12.17 KernSmooth_2.23-15 DT_0.4 promises_1.0.1 gdata_2.18.0
[36] DDRTree_0.1.5 limma_3.36.1 vegan_2.5-2 CVST_0.2-2 RcppParallel_4.4.0 Hmisc_4.1-1 ShortRead_1.38.0
[43] apcluster_1.4.7 RSpectra_0.13-1 msir_1.3.1 mnormt_1.5-5 ranger_0.10.1 digest_0.6.15 png_0.1-7
[50] qlcMatrix_0.9.7 cidr_0.1.5 cowplot_0.9.2 glmnet_2.0-16 pkgconfig_2.0.1 docopt_0.4.5 DelayedMatrixStats_1.2.0 [57] gower_0.1.2 ggbeeswarm_0.6.0 iterators_1.0.9 minqa_1.2.4 lavaan_0.6-1 reticulate_1.8 spam_2.1-4
[64] beeswarm_0.2.3 modeltools_0.2-21 RcppNumerical_0.3-2 zoo_1.8-1 tidyselect_0.2.4 clusterCrit_1.2.7 ZIM_1.0.3
[71] reshape2_1.4.3 purrr_0.2.5 kernlab_0.9-26 ica_1.0-2 pcaPP_1.9-73 EDASeq_2.14.0 viridisLite_0.3.0
[78] snow_0.4-2 rtracklayer_1.40.3 rlang_0.2.1 hexbin_1.27.2 manipulateWidget_0.9.0 NbClust_3.0 glue_1.2.0
[85] metap_0.9 RColorBrewer_1.1-2 registry_0.5 fpc_2.1-11 stringr_1.3.1 pkgmaker_0.27 lava_1.6.1
[92] fields_9.6 DESeq2_1.20.0 recipes_0.1.2 SparseM_1.77 httpuv_1.4.3 class_7.3-14 BPSC_0.99.1
[99] RMTstat_0.3 annotate_1.58.0 jsonlite_1.5 XVector_0.20.0 bit_1.1-14 mime_0.5 gridExtra_2.3
[106] gplots_3.0.1 Rsamtools_1.32.0 zingeR_0.1.0 stringi_1.2.2 gmodels_2.16.2 RcppRoll_0.3.0 gsl_1.9-10.3
[113] bitops_1.0-6 maps_3.3.0 RSQLite_2.1.1 tidyr_0.8.1 pheatmap_1.0.10 data.table_1.11.4 DEDS_1.54.0
[120] energy_1.7-4 rstudioapi_0.7 GenomicAlignments_1.16.0 sfsmisc_1.1-2 nlme_3.1-137 qvalue_2.12.0 scran_1.8.2
[127] fastcluster_1.1.25 scone_1.4.0 locfit_1.5-9.1 miniUI_0.1.1.1 cobs_1.3-3 R.oo_1.22.0 prabclus_2.2-6
[134] segmented_0.5-3.0 readxl_1.1.0 dimRed_0.1.0 timeDate_3043.102 ROTS_1.8.0 cellranger_1.1.0 munsell_0.4.3
[141] R.methodsS3_1.7.1 moments_0.14 hwriter_1.3.2 caTools_1.17.1 codetools_0.2-15 coda_0.19-1 magic_1.5-8
[148] diffusionMap_1.1-0 vipor_0.4.5 lmtest_0.9-36 htmlTable_1.12 rARPACK_0.11-0 xtable_1.8-2 SAVER_1.0.0
[155] ROCR_1.0-7 diptest_0.75-7 scatterplot3d_0.3-41 lpsymphony_1.8.0 abind_1.4-5 FNN_1.1 RANN_2.5.1
[162] sparsesvd_0.1-4 CompQuadForm_1.4.3 bibtex_0.4.2 rgl_0.99.16 tibble_1.4.2 ggdendro_0.1-20 cluster_2.0.7-1
[169] Seurat_2.3.1 Matrix_1.2-14 prettyunits_1.0.2 shinyBS_0.61 lubridate_1.7.4 ggridges_0.5.0 NOISeq_2.24.0
[176] shinydashboard_0.7.0 mclust_5.4 igraph_1.2.1 RcppEigen_0.3.3.4.0 slam_0.1-43 testthat_2.0.0 doSNOW_1.0.16
[183] geometry_0.3-6 htmltools_0.3.6 yaml_2.1.19 GenomicFeatures_1.32.0 XML_3.98-1.11 ModelMetrics_1.1.0 DrImpute_1.0
[190] foreign_0.8-70 withr_2.1.2 fitdistrplus_1.0-9 aroma.light_3.10.0 bit64_0.9-7 rngtools_1.3.1 doRNG_1.6.6
[197] foreach_1.4.4 robustbase_0.93-0 outliers_0.14 scde_2.8.0 Biostrings_2.48.0 combinat_0.0-8 iCOBRA_1.8.0
[204] memoise_1.1.0 VGAM_1.0-5 nonnest2_0.5-1 forcats_0.3.0 rio_0.5.10 geneplotter_1.58.0 permute_0.9-4
[211] caret_6.0-80 curl_3.2 fdrtool_1.2.15 trimcluster_0.1-2 acepack_1.4.1 edgeR_3.22.2 checkmate_1.8.5
[218] tensorA_0.36 DECENT_0.2.0 ellipse_0.4.1 rjson_0.2.20 openxlsx_4.1.0 ggrepel_0.8.0 distillery_1.0-4
[225] ade4_1.7-11 dtw_1.20-1 scDD_1.4.0 stabledist_0.7-1 Lmoments_1.2-3 tools_3.5.0 sandwich_2.4-0
[232] magrittr_1.5 RCurl_1.95-4.10 proxy_0.4-22 car_3.0-0 pbivnorm_0.6.0 ape_5.1 bayesm_3.1-0.1
[239] EBSeq_1.20.0 httr_1.3.1 assertthat_0.2.0 boot_1.3-20 R6_2.2.2 Rhdf5lib_1.2.1 nnet_7.3-12
[246] progress_1.1.2 tximport_1.8.0 genefilter_1.62.0 gtools_3.5.0 statmod_1.4.30 Rook_1.1-1 rhdf5_2.24.0
[253] splines_3.5.0 carData_3.0-1 colorspace_1.3-2 amap_0.8-16 NBPSeq_0.3.0 compositions_1.40-1 base64enc_0.1-3
[260] baySeq_2.14.0 pillar_1.2.3 HSMMSingleCell_0.114.0 bindrcpp_0.2.2 GenomeInfoDbData_1.1.0 plyr_1.8.4 extRemes_2.0-8
[267] dotCall64_0.9-5.2 gtable_0.2.0 zip_1.0.0 SCnorm_1.2.0 monocle_2.8.0 psych_1.8.4 knitr_1.20
[274] RcppArmadillo_0.8.500.0 latticeExtra_0.6-28 biomaRt_2.36.1 ADGofTest_0.3 copula_0.999-18 crosstalk_1.0.0 Cairo_1.5-9
[281] doParallel_1.0.11 pscl_1.5.2 flexmix_2.3-14 quantreg_5.36 AnnotationDbi_1.42.1 broom_0.4.4 scales_0.5.0
[288] arm_1.10-1 backports_1.1.2 IHW_1.8.0 densityClust_0.3 ipred_0.9-6 lme4_1.1-17 brew_1.0-6
[295] DESeq_1.32.0 Rtsne_0.13 dplyr_0.7.5 shiny_1.1.0 ddalpha_1.3.3 grid_3.5.0 numDeriv_2016.8-1
[302] bbmle_1.0.20 lazyeval_0.2.1 dynamicTreeCut_1.63-1 Formula_1.2-3 tsne_0.1-3 blockmodeling_0.3.1 DRR_0.0.3
[309] MAST_1.6.1 RUVSeq_1.14.0 viridis_0.5.1 rpart_4.1-13 zinbwave_1.2.0 compiler_3.5.0