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graphsim-1.0.0-joss.zip

TomKellyGenetics-graphsim-7b6077b
- .Rbuildignore 939 Bytes
- .circleci
  - config.yml 2.2 kB
- .github
  - ISSUE_TEMPLATE
    - feature_request.md 970 Bytes
    - general-issue.md 886 Bytes
    - report-error.md 1.8 kB
- .travis.yml 875 Bytes
- CODE_OF_CONDUCT.md 1.4 kB
- CONTRIBUTING.md 11.4 kB
- DESCRIPTION 2.0 kB
- LICENSE 35.1 kB
- NAMESPACE 1.2 kB
- NEWS.md 1.0 kB
- R
  - adjmat.R 2.3 kB
  - commonlink.R 3.3 kB
  - distance.R 6.6 kB
  - generate.R 14.5 kB
  - laplacian.R 3.1 kB
  - pi3k_akt_graph.R 517 Bytes
  - pi3k_graph.R 455 Bytes
  - plot_directed.R 10.5 kB
  - raf_mapk_graph.R 378 Bytes
  - sigma.R 15.4 kB
  - state.R 12.9 kB
  - tfgb_smad_graph.R 520 Bytes
- README.md 6.6 kB
- appveyor.yml 1.0 kB
- cran-comments.md 1.9 kB
- data
  - Pi3K_AKT_graph.rda 139.1 kB
  - Pi3K_graph.rda 1.8 kB
  - RAF_MAP_graph.rda 1.0 kB
  - TGFBeta_Smad_graph.rda 1.6 kB
- graphsim.Rproj 303 Bytes
- inst
  - CITATION 1.8 kB
- man
  - Pi3K_AKT_graph.Rd 696 Bytes
  - Pi3K_graph.Rd 622 Bytes
  - RAF_MAP_graph.Rd 557 Bytes
  - TGFBeta_Smad_graph.Rd 708 Bytes
  - generate_expression.Rd 9.0 kB
  - make_adjmatrix_graph.Rd 1.9 kB
  - make_commonlink.Rd 2.8 kB
  - make_distance.Rd 4.5 kB
  - make_laplacian.Rd 2.4 kB
  - make_sigma.Rd 9.7 kB
  - make_state_matrix.Rd 4.6 kB
  - plot_directed.Rd 4.6 kB
- paper
  - Plotsimple_graph-1.pdf 5.2 kB
  - Plotsimple_graph-2.pdf 5.2 kB
  - Plotsimulation_activating-1.pdf 5.2 kB
  - Plotsimulation_activating-2.pdf 5.4 kB
  - Plotsimulation_activating-3.pdf 5.5 kB
  - Plotsimulation_activating-4.pdf 5.5 kB
  - Plotsimulation_activating-5.pdf 12.1 kB
  - Plotsimulation_activating-6.pdf 19.2 kB
  - Plotsimulation_inhibiting-1.pdf 5.2 kB
  - Plotsimulation_inhibiting-2.pdf 5.4 kB
  - Plotsimulation_inhibiting-3.pdf 5.6 kB
  - Plotsimulation_inhibiting-4.pdf 5.5 kB
  - Plotsimulation_inhibiting-5.pdf 12.1 kB
  - Plotsimulation_inhibiting-6.pdf 19.2 kB
  - Plotsimulation_smad-1.pdf 12.2 kB
  - Plotsimulation_smad-2.pdf 10.4 kB
  - Plotsimulation_smad-3.pdf 10.7 kB
  - Plotsimulation_smad-4.pdf 11.9 kB
  - Plotsimulation_smad-5.pdf 40.5 kB
  - Plotsimulation_smad-6.pdf 40.0 kB
  - Rplot.png 10.9 kB
  - Screen Shot 2019-07-29 at 14.10.05.png 277.3 kB
  - caption.sty 4.7 kB
  - dist_mat.png 15.5 kB
  - dist_mat_pi3k.png 191.9 kB
  - dist_mat_smad_simple.png 91.1 kB
  - ex.md 3.7 kB
  - expr_cor_mat.png 15.9 kB
  - expr_cor_mat_inhibiting.png 15.7 kB
  - expr_cor_mat_inhibiting_smad_simple.png 101.7 kB
  - expr_cor_mat_pi3k.png 342.3 kB
  - expr_cor_mat_smad_simple.png 103.6 kB
  - expr_disc_mat.png 17.2 kB
  - expr_inhib_disc_mat.png 16.4 kB
  - expr_mat.png 33.3 kB
  - expr_mat_inhibiting.png 33.2 kB
  - expr_mat_inhibiting_smad_simple.png 61.3 kB
  - expr_mat_inhibiting_wide.png 395.0 kB
  - expr_mat_inhibiting_wide2.png 38.3 kB
  - expr_mat_inhibiting_wide_smad_simple.png 68.7 kB
  - expr_mat_pi3k.png 294.0 kB
  - expr_mat_pi3k2.png 302.9 kB
  - expr_mat_pi3k_wide.png 2.9 MB
  - expr_mat_smad_simple.png 60.5 kB
  - expr_mat_wide.png 399.7 kB
  - expr_mat_wide2.png 38.9 kB
  - expr_mat_wide_smad_simple.png 68.5 kB
  - figure1.pdf 85.7 kB
  - figure1.png 166.2 kB
  - figure2.pdf 787.0 kB
  - figure2.png 413.0 kB
  - figure3.pdf 808.6 kB
  - figure3.png 413.8 kB
  - figure4.pdf 325.6 kB
  - figure4.png 1.2 MB
  - generate 4.8 kB
  - graph_pi3k.png 335.6 kB
  - graph_smad_simple.png 179.6 kB
  - images.sh 74 Bytes
  - paper.Rmd 40.0 kB
  - paper.bib 15.7 kB
  - paper.json 983 Bytes
  - paper.md 28.3 kB
  - paper.pdf 530.9 kB
  - sigma_mat.png 15.6 kB
  - sigma_mat_inhibiting.png 15.5 kB
  - sigma_mat_inhibiting_smad_simple.png 101.6 kB
  - sigma_mat_pi3k.png 213.7 kB
  - sigma_mat_smad_simple.png 97.4 kB
  - simple_graph.png 24.9 kB
  - simple_graph_col.png 28.8 kB
  - simple_graph_inhibiting.png 50.7 kB
  - simple_graph_inhibiting_col.png 27.2 kB
  - state_matrix_inhibiting.png 14.8 kB
  - state_matrix_smad_simple.png 79.2 kB
  - subfig.sty 3.7 kB
- tests
  - figs
    - deps.txt 67 Bytes
    - plot-directed-graphs
      - test-plotting-directed-with-igraph.svg 3.8 kB
      - test-plotting-directed-with-plot-directed.svg 3.9 kB
      - test-plotting-directed-with-plot-directedas-state-vector.svg 3.9 kB
      - test-plotting-inhibitions-with-plot-directed-as-state-vector.svg 3.9 kB
      - test-plotting-inhibitions-with-plot-directed.svg 3.9 kB
      - test-plotting-undirected-with-igraph.svg 2.7 kB
      - test-plotting-undirected-with-plot-directed.svg 3.9 kB
      - test-plotting-with-plot-directed-parameters.svg 4.8 kB
  - testthat
    - Rplots.pdf 4.8 kB
    - test_adjmatrix.R 787 Bytes
    - test_commonlink.R 1.9 kB
    - test_distance.R 3.0 kB
    - test_generate.R 5.3 kB
    - test_laplacian.R 1.8 kB
    - test_plot.R 2.9 kB
    - test_sigma.R 9.7 kB
    - test_state.R 10.2 kB
- vignettes
  - .gitignore 11 Bytes
  - plots_directed.Rmd 10.2 kB
  - plots_directed.html 1.1 MB
  - simulate_expression.Rmd 51.8 kB
  - simulate_expression.html 2.2 MB