vignettes/miaTime.Rmd
miaTime.RmdmiaTime implements tools for time series manipulation
based on the TreeSummarizedExperiment data container.
Installing the latest development version in R.
library(devtools)
devtools::install_github("microbiome/miaTime")Loading the package:
See articles for more detailed example workflows.
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
##
## 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] miaTime_0.1.15 BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] circlize_0.4.15 systemfonts_1.0.4
## [3] plyr_1.8.7 lazyeval_0.2.2
## [5] splines_4.2.1 BiocParallel_1.31.13
## [7] GenomeInfoDb_1.33.8 ggplot2_3.3.6
## [9] scater_1.25.7 sva_3.45.0
## [11] digest_0.6.29 foreach_1.5.2
## [13] yulab.utils_0.0.5 htmltools_0.5.3
## [15] viridis_0.6.2 fansi_1.0.3
## [17] magrittr_2.0.3 memoise_2.0.1
## [19] ScaledMatrix_1.5.1 cluster_2.1.4
## [21] doParallel_1.0.17 DECIPHER_2.25.3
## [23] openxlsx_4.2.5 limma_3.53.10
## [25] ComplexHeatmap_2.13.1 Biostrings_2.65.6
## [27] annotate_1.75.0 matrixStats_0.62.0
## [29] SEtools_1.11.1 pkgdown_2.0.6
## [31] colorspace_2.0-3 ggrepel_0.9.1
## [33] blob_1.2.3 textshaping_0.3.6
## [35] xfun_0.33 dplyr_1.0.10
## [37] crayon_1.5.2 RCurl_1.98-1.9
## [39] jsonlite_1.8.2 genefilter_1.79.0
## [41] survival_3.4-0 iterators_1.0.14
## [43] ape_5.6-2 glue_1.6.2
## [45] registry_0.5-1 gtable_0.3.1
## [47] zlibbioc_1.43.0 XVector_0.37.1
## [49] GetoptLong_1.0.5 DelayedArray_0.23.2
## [51] V8_4.2.1 BiocSingular_1.13.1
## [53] shape_1.4.6 SingleCellExperiment_1.19.1
## [55] BiocGenerics_0.43.4 scales_1.2.1
## [57] pheatmap_1.0.12 DBI_1.1.3
## [59] edgeR_3.39.6 randomcoloR_1.1.0.1
## [61] Rcpp_1.0.9 viridisLite_0.4.1
## [63] xtable_1.8-4 decontam_1.17.0
## [65] clue_0.3-61 tidytree_0.4.1
## [67] rsvd_1.0.5 bit_4.0.4
## [69] stats4_4.2.1 httr_1.4.4
## [71] RColorBrewer_1.1-3 scuttle_1.7.4
## [73] pkgconfig_2.0.3 XML_3.99-0.11
## [75] sass_0.4.2 locfit_1.5-9.6
## [77] utf8_1.2.2 reshape2_1.4.4
## [79] tidyselect_1.2.0 rlang_1.0.6
## [81] AnnotationDbi_1.59.1 munsell_0.5.0
## [83] tools_4.2.1 cachem_1.0.6
## [85] cli_3.4.1 DirichletMultinomial_1.39.0
## [87] generics_0.1.3 RSQLite_2.2.18
## [89] mia_1.5.17 evaluate_0.17
## [91] stringr_1.4.1 fastmap_1.1.0
## [93] yaml_2.3.5 ragg_1.2.3
## [95] knitr_1.40 bit64_4.0.5
## [97] fs_1.5.2 zip_2.2.1
## [99] purrr_0.3.5 KEGGREST_1.37.3
## [101] sparseMatrixStats_1.9.0 nlme_3.1-159
## [103] compiler_4.2.1 beeswarm_0.4.0
## [105] curl_4.3.3 png_0.1-7
## [107] treeio_1.21.2 tibble_3.1.8
## [109] geneplotter_1.75.0 bslib_0.4.0
## [111] stringi_1.7.8 desc_1.4.2
## [113] lattice_0.20-45 Matrix_1.5-1
## [115] sechm_1.5.1 permute_0.9-7
## [117] vegan_2.6-5 vctrs_0.4.2
## [119] pillar_1.8.1 lifecycle_1.0.3
## [121] BiocManager_1.30.18 jquerylib_0.1.4
## [123] GlobalOptions_0.1.2 BiocNeighbors_1.15.1
## [125] irlba_2.3.5.1 data.table_1.14.2
## [127] bitops_1.0-7 seriation_1.3.6
## [129] GenomicRanges_1.49.1 R6_2.5.1
## [131] bookdown_0.29 TSP_1.2-1
## [133] gridExtra_2.3 vipor_0.4.5
## [135] IRanges_2.31.2 codetools_0.2-18
## [137] MASS_7.3-58.1 TreeSummarizedExperiment_2.1.4
## [139] SummarizedExperiment_1.27.3 DESeq2_1.37.6
## [141] rprojroot_2.0.3 rjson_0.2.21
## [143] S4Vectors_0.35.4 GenomeInfoDbData_1.2.9
## [145] MultiAssayExperiment_1.23.9 mgcv_1.8-40
## [147] parallel_4.2.1 beachmat_2.13.4
## [149] grid_4.2.1 tidyr_1.2.1
## [151] DelayedMatrixStats_1.19.2 rmarkdown_2.17
## [153] MatrixGenerics_1.9.1 Rtsne_0.16
## [155] Biobase_2.57.1 ggbeeswarm_0.6.0