Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programs

This GitHub page provide R scripts developped for Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes.

The different scripts were used under :

• R version 4.2.2 (2022-10-31 ucrt)
• Platform: x86_64-w64-mingw32/x64 (64-bit)
• Running under: Windows 10 x64 (build 19044)

packages used:

• ade4_1.7-22
• adegenet_2.1.10
• ape_5.6-2
• aplot_0.1.9
• assertthat_0.2.1
• backports_1.4.1
• bio3d_2.4-4
• BiocGenerics_0.44.0
• BiocManager_1.30.19
• BiocParallel_1.32.5
• Biostrings_2.66.0
• bit_4.0.5
• bit64_4.0.5
• bitops_1.0-7
• blob_1.2.3
• broom_1.0.3
• cachem_1.0.6
• castor_1.7.6
• cellranger_1.1.0
• circlize_0.4.15
• cli_3.6.0
• clue_0.3-64
• cluster_2.1.4
• clusterGeneration_1.3.7
• coda_0.19-4
• codetools_0.2-19
• colorspace_2.1-0
• combinat_0.0-8
• compiler_4.2.2
• ComplexHeatmap_2.14.0
• corpcor_1.6.10
• crayon_1.5.2
• data.table_1.14.6
• DBI_1.1.3
• dbplyr_2.3.0
• DECIPHER_2.26.0
• digest_0.6.31
• doParallel_1.0.17
• ellipse_0.4.3
• ellipsis_0.3.2
• expm_0.999-7
• fansi_1.0.4
• fastmap_1.1.0
• fastmatch_1.1-3
• forcats_1.0.0
• foreach_1.5.2
• formatR_1.14
• fs_1.6.1
• futile.logger_1.4.3
• futile.options_1.0.1
• gargle_1.3.0
• gaston_1.5.9
• generics_0.1.3
• GenomeInfoDbData_1.2.9
• GetoptLong_1.0.5
• ggfun_0.0.9
• ggplot2_3.4.1
• ggplotify_0.1.0
• ggrepel_0.9.3
• GlobalOptions_0.1.2
• glue_1.6.2
• googledrive_2.0.0
• googlesheets4_1.0.1
• gridExtra_2.3
• gridGraphics_0.5-1
• gtable_0.3.1
• haven_2.5.1
• hms_1.1.2
• htmltools_0.5.4
• httpuv_1.6.8
• httr_1.4.4
• igraph_1.4.0
• IRanges_2.32.0
• iterators_1.0.14
• jsonlite_1.8.4
• lambda.r_1.2.4
• later_1.3.0
• lazyeval_0.2.2
• lifecycle_1.0.3
• lubridate_1.9.2
• magrittr_2.0.3
• maps_3.4.1
• MASS_7.3-58.2
• Matrix_1.5-3
• matrixStats_0.63.0
• memoise_2.0.1
• mgcv_1.8-41
• mime_0.12
• mixOmics_6.22.0
• mnormt_2.1.1
• modelr_0.1.10
• munsell_0.5.0
• naturalsort_0.1.3
• nlme_3.1-162
• numDeriv_2016.8-1.1
• optimParallel_1.0-2
• patchwork_1.1.2
• permute_0.9-7
• phangorn_2.11.1
• phylobase_0.8.10
• phytools_1.2-0
• pillar_1.8.1
• pkgconfig_2.0.3
• plotrix_3.8-2
• plyr_1.8.8
• png_0.1-8
• prettyunits_1.1.1
• progress_1.2.2
• promises_1.2.0.1
• quadprog_1.5-8
• R6_2.5.1
• rARPACK_0.11-0
• RColorBrewer_1.1-3
• RCurl_1.98-1.10
• readr_2.1.4
• readxl_1.4.2
• reprex_2.0.2
• reshape2_1.4.4
• rjson_0.2.21
• rlang_1.0.6
• rncl_0.8.7
• RNeXML_2.4.11
• RSpectra_0.16-1
• RSQLite_2.2.20
• rstudioapi_0.14
• rvest_1.0.3
• S4Vectors_0.36.1
• scales_1.2.1
• scatterplot3d_0.3-42
• seqinr_4.2-23
• shape_1.4.6
• shiny_1.7.4
• splines_4.2.2
• stringi_1.7.12
• stringr_1.5.0
• tibble_3.1.8
• tidyr_1.3.0
• tidyselect_1.2.0
• tidytree_0.4.2
• tidyverse_1.3.2
• timechange_0.2.0
• tools_4.2.2
• treeio_1.22.0
• tzdb_0.3.0
• UpSetR_1.4.0
• utf8_1.2.3
• uuid_1.1-0
• vctrs_0.5.2
• vegan_2.6-4
• VennDiagram_1.7.3
• wesanderson_0.3.6
• withr_2.5.0
• XML_3.99-0.13
• xml2_1.3.3
• xtable_1.8-4
• XVector_0.38.0
• yulab.utils_0.0.6
• zlibbioc_1.44.0

Authors

• Cyril Libourel (cyril.libourel@gmail.com)