DART-ID
Code for figures/data analysis of the DART-ID publication:
While the DART-ID software is written in Python, all downstream analyses, as well as the first version of DART, are written in R. Some analysis and software development was also done with iPython notebooks.
All figures can be generated with the scripts in Rscripts/fig_scripts
Data
All data referenced in this code is available on MassIVE (ID: MSV000083149). evidence_updated.txt files referenced are from the alignment results, located in MSV000083149/other/Alignments (ftp://massive.ucsd.edu/MSV000083149/other/Alignments/). R Data files can be found at MSV000083149/other/Rdata (ftp://massive.ucsd.edu/MSV000083149/other/Rdata/).
Help
All R code was run on the following R session:
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 ggridges_0.5.0 viridisLite_0.3.0 bindrcpp_0.2.2 pracma_2.1.5 forcats_0.3.0 stringr_1.3.1
[8] dplyr_0.7.6 purrr_0.2.5 readr_1.1.1 tidyr_0.8.1 tibble_1.4.2 ggplot2_3.0.0 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 cellranger_1.1.0 pillar_1.3.0 compiler_3.4.4 plyr_1.8.4 bindr_0.1.1 tools_3.4.4 jsonlite_1.5
[9] lubridate_1.7.4 nlme_3.1-137 gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.2 rlang_0.2.2 cli_1.0.0 rstudioapi_0.7
[17] yaml_2.2.0 haven_1.1.2 withr_2.1.2 xml2_1.2.0 httr_1.3.1 hms_0.4.2 grid_3.4.4 tidyselect_0.2.4
[25] glue_1.3.0 R6_2.2.2 fansi_0.3.0 readxl_1.1.0 modelr_0.1.2 magrittr_1.5 backports_1.1.2 scales_1.0.0
[33] rvest_0.3.2 assertthat_0.2.0 colorspace_1.3-2 utf8_1.1.4 stringi_1.2.4 lazyeval_0.2.1 munsell_0.5.0 broom_0.5.0
[41] crayon_1.3.4
Python code was run on Python 3.6.6 on an Anaconda3 distribution, with the following (relevant) packages:
anaconda 2018.12 py27_0
anaconda-client 1.7.2 py27_0
conda 4.5.12 py27_0
conda-build 3.17.6 py27_0
cython 0.29.2 py27h0a44026_0
ipykernel 4.10.0 py27_0
ipython 5.8.0 py27_0
ipython_genutils 0.2.0 py27h8b9a179_0
ipywidgets 7.4.2 py27_0
jupyter 1.0.0 py27_7
jupyter_client 5.2.4 py27_0
jupyter_console 5.2.0 py27_1
jupyter_core 4.4.0 py27_0
jupyterlab 0.33.11 py27_0
jupyterlab_launcher 0.11.2 py27h28b3542_0
matplotlib 2.2.3 py27h54f8f79_0
networkx 2.2 py27_1
numpy 1.15.4 py27hacdab7b_0
numpy-base 1.15.4 py27h6575580_0
pip 18.1 py27_0
pytest 4.0.2 py27_0
scikit-learn 0.20.1 py27h27c97d8_0
scipy 1.1.0 py27h1410ff5_2
setuptools 40.6.3 py27_0
tk 8.6.8 ha441bb4_0
yaml 0.1.7 hc338f04_2