This is the repository archiving code and data for MsRDB manuscript -- Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data
The "MsRDB" directory contains files for algorithms and results. Algorithm.R includes the code of new MsRDB test, ASVwise.R includes the code of RDb test and KNN-RDB test, and MultiATE.R includes the code of a generalized version of ATE function in ATE package. Simulation.R includes code of numerical experiments and visualization in Section 2.2, Vangay_Cell_2018.R includes code of numerical experiments and visualization in Section 2.3, and Bokulich_PNAS_2013.R includes code of numerical experiments and visualization in Section 2.4.
The "Data" directory contains all data set used in the manuscript.
First, run all code in Algorithm.R, ASVwise.R and MultiATE.R. Then, the results can be replicated by running one of Simulation.R, Vangay_Cell_2018.R, and Bokulich_PNAS_2013.R.
R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS 12.0.1
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] doRNG_1.8.2 rngtools_1.5 doParallel_1.0.16 iterators_1.0.13 foreach_1.5.1 microbiome_1.14.0 ALDEx2_1.24.0
[8] Rfast_2.0.3 RcppZiggurat_0.1.6 zCompositions_1.3.4 truncnorm_1.0-8 NADA_1.6-1.1 survival_3.2-12 MASS_7.3-54
[15] ANCOMBC_1.2.2 phyloseq_1.36.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.0.1
[22] tidyr_1.1.3 tibble_3.1.3 ggplot2_3.3.5 tidyverse_1.3.1 biomformat_1.20.0 igraph_1.2.6 DECIPHER_2.20.0
[29] RSQLite_2.2.8 Biostrings_2.60.2 GenomeInfoDb_1.28.1 XVector_0.32.0 IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0
[36] kmer_1.1.2 dada2_1.20.0 Rcpp_1.0.7
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 plyr_1.8.6 splines_4.1.0 BiocParallel_1.26.2
[6] digest_0.6.27 fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0 cluster_2.1.2
[11] tzdb_0.1.2 modelr_0.1.8 RcppParallel_5.1.4 matrixStats_0.60.1 jpeg_0.1-9
[16] colorspace_2.0-2 blob_1.2.2 rvest_1.0.1 haven_2.4.3 rbibutils_2.2.3
[21] crayon_1.4.1 RCurl_1.98-1.4 jsonlite_1.7.2 ape_5.5 glue_1.4.2
[26] gtable_0.3.0 phylogram_2.1.0 zlibbioc_1.38.0 DelayedArray_0.18.0 Rhdf5lib_1.14.2
[31] scales_1.1.1 futile.options_1.0.1 DBI_1.1.1 bit_4.0.4 httr_1.4.2
[36] RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0 dbplyr_2.1.1
[41] utf8_1.2.2 tidyselect_1.1.1 labeling_0.4.2 rlang_0.4.11 reshape2_1.4.4
[46] munsell_0.5.0 cellranger_1.1.0 tools_4.1.0 cachem_1.0.6 cli_3.0.1
[51] generics_0.1.0 ade4_1.7-17 broom_0.7.9 fastmap_1.1.0 bit64_4.0.5
[56] fs_1.5.0 nlme_3.1-152 formatR_1.11 xml2_1.3.2 compiler_4.1.0
[61] rstudioapi_0.13 png_0.1-7 reprex_2.0.1 stringi_1.7.3 futile.logger_1.4.3
[66] lattice_0.20-44 Matrix_1.3-4 nloptr_1.2.2.2 vegan_2.5-7 permute_0.9-5
[71] multtest_2.48.0 vctrs_0.3.8 pillar_1.6.2 lifecycle_1.0.0 rhdf5filters_1.4.0
[76] Rdpack_2.1.2 data.table_1.14.0 bitops_1.0-7 GenomicRanges_1.44.0 R6_2.5.1
[81] latticeExtra_0.6-29 hwriter_1.3.2 ShortRead_1.50.0 codetools_0.2-18 lambda.r_1.2.4
[86] assertthat_0.2.1 rhdf5_2.36.0 SummarizedExperiment_1.22.0 withr_2.4.2 GenomicAlignments_1.28.0
[91] Rsamtools_2.8.0 GenomeInfoDbData_1.2.6 mgcv_1.8-36 hms_1.1.0 grid_4.1.0
[96] MatrixGenerics_1.4.2 Rtsne_0.15 Biobase_2.52.0 lubridate_1.7.10