MF9155 Introduction to statistics and bioinformatics for the analysis of large-scale biological data
The environment.yml file contains packages from a course at University of Oslo:
Introduction to statistics and bioinformatics for the analysis of large-scale biological data
Create conda environment:
conda env create -f MF9155_env.yml
If you add something to the file, update the environment:
conda env update -f MF9155_env.yml
To run R with the installed packages, first activate environment:
conda activate MF9155_course
Tell RStudio which R path to use:
export RSTUDIO_WHICH_R=`which R`
Then run RStudio:
rstudio
Deactivate environment when you're done:
conda deactivate
The list_packages.R script loads all the packages needed for the course, and runs sessionInfo(). Output:
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fo_FO.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=fo_FO.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=fo_FO.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fo_FO.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] microbenchmark_1.4-7 logging_0.10-108
[3] dplR_1.7.0 yaml_2.2.0
[5] rjson_0.2.20 optparse_1.6.4
[7] data.table_1.12.6 reshape2_1.4.3
[9] forcats_0.4.0 stringr_1.4.0
[11] dplyr_0.8.3 purrr_0.3.3
[13] readr_1.3.1 tidyr_1.0.0
[15] tibble_2.1.3 tidyverse_1.3.0
[17] fitdistrplus_1.0-14 npsurv_0.4-0
[19] lsei_1.2-0 MASS_7.3-51.4
[21] seqinr_3.6-1 rtracklayer_1.44.4
[23] Gviz_1.28.3 gcrma_2.56.0
[25] affy_1.62.0 Biostrings_2.52.0
[27] XVector_0.24.0 GEOquery_2.52.0
[29] biomaRt_2.40.5 hgu133plus2.db_3.2.3
[31] org.Hs.eg.db_3.8.2 AnnotationDbi_1.46.1
[33] VennDiagram_1.6.20 futile.logger_1.4.3
[35] genefilter_1.66.0 psych_1.8.12
[37] Hmisc_4.3-0 ggplot2_3.2.1
[39] Formula_1.2-3 survival_2.44-1.1
[41] lattice_0.20-38 ModelGood_1.0.9
[43] randomForestSRC_2.9.2 glmnet_3.0-1
[45] Matrix_1.2-17 DESeq2_1.24.0
[47] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
[49] BiocParallel_1.18.1 matrixStats_0.55.0
[51] Biobase_2.44.0 GenomicRanges_1.36.1
[53] GenomeInfoDb_1.20.0 IRanges_2.18.3
[55] S4Vectors_0.22.1 BiocGenerics_0.30.0
[57] edgeR_3.26.8 limma_3.40.6
[59] RColorBrewer_1.1-2 ConsensusClusterPlus_1.48.0
[61] cluster_2.1.0 pheatmap_1.0.12
[63] BiocManager_1.30.10 devtools_2.2.1
[65] usethis_1.5.1
loaded via a namespace (and not attached):
[1] R.utils_2.9.0 tidyselect_0.2.5 RSQLite_2.1.2
[4] htmlwidgets_1.5.1 munsell_0.5.0 codetools_0.2-16
[7] preprocessCore_1.46.0 withr_2.1.2 colorspace_1.4-1
[10] knitr_1.26 rstudioapi_0.10 GenomeInfoDbData_1.2.1
[13] mnormt_1.5-5 bit64_0.9-7 rprojroot_1.3-2
[16] vctrs_0.2.0 generics_0.0.2 lambda.r_1.2.4
[19] xfun_0.11 biovizBase_1.32.0 R6_2.4.1
[22] locfit_1.5-9.1 AnnotationFilter_1.8.0 bitops_1.0-6
[25] assertthat_0.2.1 scales_1.1.0 nnet_7.3-12
[28] gtable_0.3.0 processx_3.4.1 ensembldb_2.8.1
[31] rlang_0.4.2 zeallot_0.1.0 splines_3.6.1
[34] lazyeval_0.2.2 acepack_1.4.1 dichromat_2.0-0
[37] broom_0.5.2 checkmate_1.9.4 modelr_0.1.5
[40] GenomicFeatures_1.36.4 backports_1.1.5 tools_3.6.1
[43] affyio_1.54.0 ellipsis_0.3.0 sessioninfo_1.1.1
[46] plyr_1.8.4 Rcpp_1.0.3 base64enc_0.1-3
[49] progress_1.2.2 zlibbioc_1.30.0 RCurl_1.95-4.12
[52] ps_1.3.0 prettyunits_1.0.2 rpart_4.1-15
[55] haven_2.2.0 fs_1.3.1 magrittr_1.5
[58] futile.options_1.0.1 reprex_0.3.0 ProtGenerics_1.16.0
[61] pkgload_1.0.2 hms_0.5.2 xtable_1.8-4
[64] XML_3.98-1.20 readxl_1.3.1 gridExtra_2.3
[67] shape_1.4.4 testthat_2.3.0 compiler_3.6.1
[70] crayon_1.3.4 R.oo_1.23.0 htmltools_0.4.0
[73] geneplotter_1.62.0 lubridate_1.7.4 DBI_1.0.0
[76] formatR_1.7 dbplyr_1.4.2 getopt_1.20.3
[79] ade4_1.7-13 cli_1.1.0 R.methodsS3_1.7.1
[82] pkgconfig_2.0.3 GenomicAlignments_1.20.1 signal_0.7-6
[85] foreign_0.8-72 xml2_1.2.2 foreach_1.4.7
[88] annotate_1.62.0 rvest_0.3.5 VariantAnnotation_1.30.1
[91] callr_3.3.2 digest_0.6.23 cellranger_1.1.0
[94] htmlTable_1.13.2 curl_4.2 Rsamtools_2.0.3
[97] lifecycle_0.1.0 nlme_3.1-142 jsonlite_1.6
[100] desc_1.2.0 BSgenome_1.52.0 pillar_1.4.2
[103] httr_1.4.1 pkgbuild_1.0.6 glue_1.3.1
[106] remotes_2.1.0 png_0.1-7 iterators_1.0.12
[109] bit_1.1-14 stringi_1.4.3 blob_1.2.0
[112] latticeExtra_0.6-28 memoise_1.1.0