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bvieth / powsimR

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.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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Not all packages installed? #27

Closed virenp closed 5 years ago

virenp commented 5 years ago

Hello. Not sure if this is an issue. The website shows 331 lines of tools/packages after installation. My installation shows only 305. Would this be due to R version?

library(powsimR) Loading required package: gamlss.dist Loading required package: MASS Warning messages: 1: replacing previous import ‘DECENT::lrTest’ by ‘MAST::lrTest’ when loading ‘powsimR’ 2: replacing previous import ‘parallel::makeCluster’ by ‘snow::makeCluster’ when loading ‘powsimR’ 3: replacing previous import ‘parallel::stopCluster’ by ‘snow::stopCluster’ when loading ‘powsimR’ 4: replacing previous import ‘penalized::predict’ by ‘stats::predict’ when loading ‘powsimR’ 5: replacing previous import ‘zinbwave::glmWeightedF’ by ‘zingeR::glmWeightedF’ when loading ‘powsimR’ sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Scientific Linux 7.3 (Nitrogen)

Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2

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] powsimR_1.1.2 gamlss.dist_5.0-6 MASS_7.3-50

loaded via a namespace (and not attached): [1] mixtools_1.1.0 softImpute_1.4 [3] minpack.lm_1.2-1 pbapply_1.3-4 [5] lattice_0.20-35 haven_1.1.2 [7] fastICA_1.2-1 mgcv_1.8-24 [9] penalized_0.9-51 blob_1.1.1 [11] survival_2.42-6 later_0.7.3 [13] nloptr_1.0.4 DBI_1.0.0 [15] R.utils_2.6.0 SingleCellExperiment_1.0.0 [17] Linnorm_2.2.0 bindr_0.1.1 [19] zlibbioc_1.24.0 MatrixModels_0.4-1 [21] pspline_1.0-18 pcaMethods_1.70.0 [23] SDMTools_1.1-221 htmlwidgets_1.2 [25] mvtnorm_1.0-8 hdf5r_1.0.0 [27] UpSetR_1.3.3 parallel_3.4.3 [29] scater_1.6.3 irlba_2.3.2 [31] DEoptimR_1.0-8 lars_1.2 [33] Rcpp_0.12.18 KernSmooth_2.23-15 [35] DT_0.4 promises_1.0.1 [37] gdata_2.18.0 DDRTree_0.1.5 [39] DelayedArray_0.4.1 limma_3.34.9 [41] vegan_2.5-2 Hmisc_4.1-1 [43] ShortRead_1.36.1 apcluster_1.4.7 [45] RSpectra_0.13-1 msir_1.3.1 [47] mnormt_1.5-5 digest_0.6.15 [49] RMySQL_0.10.15 png_0.1-7 [51] qlcMatrix_0.9.7 cowplot_0.9.3 [53] glmnet_2.0-16 pkgconfig_2.0.1 [55] docopt_0.6 ggbeeswarm_0.6.0 [57] iterators_1.0.10 minqa_1.2.4 [59] lavaan_0.6-2 reticulate_1.10 [61] SummarizedExperiment_1.8.1 spam_2.2-0 [63] beeswarm_0.2.3 modeltools_0.2-22 [65] RcppNumerical_0.3-2 zoo_1.8-3 [67] tidyselect_0.2.4 ZIM_1.0.3 [69] reshape2_1.4.3 purrr_0.2.5 [71] kernlab_0.9-26 ica_1.0-2 [73] pcaPP_1.9-73 EDASeq_2.12.0 [75] viridisLite_0.3.0 snow_0.4-2 [77] rtracklayer_1.38.3 rlang_0.2.1 [79] hexbin_1.27.2 manipulateWidget_0.10.0 [81] glue_1.3.0 metap_1.0 [83] RColorBrewer_1.1-2 registry_0.5 [85] fpc_2.1-11.1 matrixStats_0.54.0 [87] stringr_1.3.1 pkgmaker_0.27 [89] fields_9.6 DESeq2_1.18.1 [91] SparseM_1.77 gbRd_0.4-11 [93] httpuv_1.4.5 class_7.3-14 [95] BPSC_0.99.1 RMTstat_0.3 [97] annotate_1.56.2 webshot_0.5.0 [99] jsonlite_1.5 XVector_0.18.0 [101] bit_1.1-14 mime_0.5 [103] gridExtra_2.3 gplots_3.0.1 [105] Rsamtools_1.30.0 zingeR_0.1.0 [107] stringi_1.2.4 gmodels_2.18.1 [109] gsl_1.9-10.3 bitops_1.0-6 [111] Rdpack_0.9-0 maps_3.3.0 [113] RSQLite_2.1.1 tidyr_0.8.1 [115] pheatmap_1.0.10 data.table_1.11.4 [117] DEDS_1.52.0 energy_1.7-4 [119] rstudioapi_0.7 GenomicAlignments_1.14.2 [121] nlme_3.1-137 qvalue_2.10.0 [123] scran_1.6.9 fastcluster_1.1.25 [125] locfit_1.5-9.1 scone_1.2.0 [127] miniUI_0.1.1.1 cobs_1.3-3 [129] R.oo_1.22.0 prabclus_2.2-6 [131] segmented_0.5-3.0 BiocGenerics_0.24.0 [133] readxl_1.1.0 ROTS_1.6.0 [135] munsell_0.5.0 cellranger_1.1.0 [137] R.methodsS3_1.7.1 moments_0.14 [139] hwriter_1.3.2 caTools_1.17.1.1 [141] codetools_0.2-15 coda_0.19-1 [143] Biobase_2.38.0 GenomeInfoDb_1.14.0 [145] vipor_0.4.5 lmtest_0.9-36 [147] htmlTable_1.12 rARPACK_0.11-0 [149] xtable_1.8-2 SAVER_1.0.0 [151] ROCR_1.0-7 diptest_0.75-7 [153] lpsymphony_1.7.1 abind_1.4-5 [155] FNN_1.1.2 RANN_2.6 [157] sparsesvd_0.1-4 CompQuadForm_1.4.3 [159] GenomicRanges_1.30.3 bibtex_0.4.2 [161] rgl_0.99.16 tibble_1.4.2 [163] ggdendro_0.1-20 cluster_2.0.7-1 [165] Seurat_2.3.4 Matrix_1.2-14 [167] prettyunits_1.0.2 shinyBS_0.61 [169] ggridges_0.5.0 NOISeq_2.22.1 [171] shinydashboard_0.7.0 mclust_5.4.1 [173] igraph_1.2.2 slam_0.1-43 [175] testthat_2.0.0 doSNOW_1.0.16 [177] htmltools_0.3.6 GenomicFeatures_1.30.3 [179] XML_3.98-1.13 DrImpute_1.0 [181] foreign_0.8-71 withr_2.1.2 [183] fitdistrplus_1.0-9 BiocParallel_1.12.0 [185] aroma.light_3.8.0 bit64_0.9-7 [187] rngtools_1.3.1 doRNG_1.7.1 [189] foreach_1.4.4 robustbase_0.93-2 [191] outliers_0.14 scde_2.6.0 [193] Biostrings_2.46.0 combinat_0.0-8 [195] iCOBRA_1.6.0 memoise_1.1.0 [197] VGAM_1.0-5 nonnest2_0.5-1 [199] forcats_0.3.0 rio_0.5.10 [201] geneplotter_1.56.0 permute_0.9-4 [203] curl_3.2 fdrtool_1.2.15 [205] trimcluster_0.1-2.1 acepack_1.4.1 [207] edgeR_3.20.9 checkmate_1.8.5 [209] tensorA_0.36.1 DECENT_0.2.0 [211] ellipse_0.4.1 ggplot2_3.0.0 [213] rjson_0.2.20 openxlsx_4.1.0 [215] ggrepel_0.8.0 distillery_1.0-4 [217] dtw_1.20-1 scDD_1.2.0 [219] stabledist_0.7-1 Lmoments_1.2-3 [221] tools_3.4.3 sandwich_2.4-0 [223] magrittr_1.5 RCurl_1.95-4.11 [225] proxy_0.4-22 car_3.0-0 [227] pbivnorm_0.6.0 ape_5.1 [229] bayesm_3.1-0.1 EBSeq_1.18.0 [231] httr_1.3.1 assertthat_0.2.0 [233] boot_1.3-20 R6_2.2.2 [235] nnet_7.3-12 progress_1.2.0 [237] tximport_1.6.0 genefilter_1.60.0 [239] gtools_3.8.1 statmod_1.4.30 [241] Rook_1.1-1 rhdf5_2.22.0 [243] splines_3.4.3 carData_3.0-1 [245] colorspace_1.3-2 amap_0.8-16 [247] stats4_3.4.3 NBPSeq_0.3.0 [249] compositions_1.40-2 base64enc_0.1-3 [251] baySeq_2.12.0 pillar_1.3.0 [253] HSMMSingleCell_0.112.0 bindrcpp_0.2.2 [255] GenomeInfoDbData_1.0.0 plyr_1.8.4 [257] extRemes_2.0-9 dotCall64_1.0-0 [259] gtable_0.2.0 zip_1.0.0 [261] SCnorm_1.0.0 monocle_2.6.4 [263] knitr_1.20 RcppArmadillo_0.8.600.0.0 [265] latticeExtra_0.6-28 biomaRt_2.34.2 [267] IRanges_2.12.0 ADGofTest_0.3 [269] copula_0.999-18 crosstalk_1.0.0 [271] Cairo_1.5-9 doParallel_1.0.11 [273] pscl_1.5.2 flexmix_2.3-14 [275] quantreg_5.36 AnnotationDbi_1.40.0 [277] broom_0.5.0 scales_0.5.0 [279] arm_1.10-1 backports_1.1.2 [281] IHW_1.6.0 S4Vectors_0.16.0 [283] densityClust_0.3 lme4_1.1-17 [285] brew_1.0-6 hms_0.4.2 [287] DESeq_1.30.0 Rtsne_0.13 [289] dplyr_0.7.6 shiny_1.1.0 [291] grid_3.4.3 numDeriv_2016.8-1 [293] bbmle_1.0.20 lazyeval_0.2.1 [295] dynamicTreeCut_1.63-1 Formula_1.2-3 [297] tsne_0.1-3 blockmodeling_0.3.1 [299] crayon_1.3.4 MAST_1.4.1 [301] RUVSeq_1.12.0 viridis_0.5.1 [303] rpart_4.1-13 zinbwave_1.0.0 [305] compiler_3.4.3

bvieth commented 5 years ago

Hello,

so the lines of the sessionInfo() is not from a cleaned up installation on my system, ie. that also other packages that I have installed are printed. Since you have powsimR listed as attached you should be ready to go.

Kind regards Beate