Files in TomKellyGenetics/graphsim
Simulate Expression Data from 'igraph' Networks
.Rbuildignore
.circleci/config.yml
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/general-issue.md
.github/ISSUE_TEMPLATE/report-error.md
.travis.yml
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
Meta/vignette.rds
NAMESPACE
NEWS.md
R/adjmat.R
R/commonlink.R
R/distance.R
R/generate.R
R/graphsim-package.R
R/laplacian.R
R/pi3k_akt_graph.R
R/pi3k_graph.R
R/plot_directed.R
R/raf_mapk_graph.R
R/sigma.R
R/state.R
R/tfgb_smad_graph.R
README.md
appveyor.yml
cran-comments.md
data/Pi3K_AKT_graph.rda
data/Pi3K_graph.rda
data/RAF_MAP_graph.rda
data/TGFBeta_Smad_graph.rda
graphsim.Rproj
inst/CITATION
man/Pi3K_AKT_graph.Rd
man/Pi3K_graph.Rd
man/RAF_MAP_graph.Rd
man/TGFBeta_Smad_graph.Rd
man/generate_expression.Rd
man/graphsim-package.Rd
man/make_adjmatrix.Rd
man/make_commonlink.Rd
man/make_distance.Rd
man/make_laplacian.Rd
man/make_sigma.Rd
man/make_state.Rd
man/plot_directed.Rd
paper/Plotsimple_graph-1.pdf
paper/Plotsimple_graph-2.pdf
paper/Plotsimulation_activating-1.pdf
paper/Plotsimulation_activating-2.pdf
paper/Plotsimulation_activating-3.pdf
paper/Plotsimulation_activating-4.pdf
paper/Plotsimulation_activating-5.pdf
paper/Plotsimulation_inhibiting-1.pdf
paper/Plotsimulation_inhibiting-2.pdf
paper/Plotsimulation_inhibiting-3.pdf
paper/Plotsimulation_inhibiting-4.pdf
paper/Plotsimulation_inhibiting-5.pdf
paper/Plotsimulation_smad-1.pdf
paper/Plotsimulation_smad-2.pdf
paper/Plotsimulation_smad-3.pdf
paper/Plotsimulation_smad-4.pdf
paper/Plotsimulation_smad-5.pdf
paper/Rplot.png
paper/Screen Shot 2019-07-29 at 14.10.05.png
paper/caption.sty
paper/dist_mat.png
paper/dist_mat_pi3k.png
paper/dist_mat_smad_simple.png
paper/ex.md
paper/expr_cor_mat.png
paper/expr_cor_mat_inhibiting.png
paper/expr_cor_mat_inhibiting_smad_simple.png
paper/expr_cor_mat_pi3k.png
paper/expr_cor_mat_smad_simple.png
paper/expr_disc_mat.png
paper/expr_inhib_disc_mat.png
paper/expr_mat.png
paper/expr_mat_inhibiting.png
paper/expr_mat_inhibiting_smad_simple.png
paper/expr_mat_inhibiting_wide.png
paper/expr_mat_inhibiting_wide2.png
paper/expr_mat_inhibiting_wide_smad_simple.png
paper/expr_mat_pi3k.png
paper/expr_mat_pi3k2.png
paper/expr_mat_pi3k_wide.png
paper/expr_mat_smad_simple.png
paper/expr_mat_wide.png
paper/expr_mat_wide2.png
paper/expr_mat_wide_smad_simple.png
paper/figure1.pdf
paper/figure1.png
paper/figure2.pdf
paper/figure2.png
paper/figure3.pdf
paper/figure3.png
paper/figure4.pdf
paper/figure4.png
paper/generate
paper/graph_pi3k.png
paper/graph_smad_simple.png
paper/images.sh
paper/paper.Rmd
paper/paper.bib
paper/paper.json
paper/paper.md
paper/paper.pdf
paper/sigma_mat.png
paper/sigma_mat_inhibiting.png
paper/sigma_mat_inhibiting_smad_simple.png
paper/sigma_mat_pi3k.png
paper/sigma_mat_smad_simple.png
paper/simple_graph.png
paper/simple_graph_col.png
paper/simple_graph_inhibiting.png
paper/simple_graph_inhibiting_col.png
paper/state_matrix_inhibiting.png
paper/state_matrix_smad_simple.png
paper/subfig.sty
tests/figs/deps.txt
tests/figs/plot-directed-graphs/test-plotting-directed-with-igraph.svg
tests/figs/plot-directed-graphs/test-plotting-directed-with-plot-directed.svg
tests/figs/plot-directed-graphs/test-plotting-directed-with-plot-directedas-state-vector.svg
tests/figs/plot-directed-graphs/test-plotting-inhibitions-with-plot-directed-as-state-vector.svg
tests/figs/plot-directed-graphs/test-plotting-inhibitions-with-plot-directed.svg
tests/figs/plot-directed-graphs/test-plotting-undirected-with-igraph.svg
tests/figs/plot-directed-graphs/test-plotting-undirected-with-plot-directed.svg
tests/figs/plot-directed-graphs/test-plotting-with-plot-directed-parameters.svg
tests/testthat/Rplots.pdf
tests/testthat/test_adjmatrix.R
tests/testthat/test_commonlink.R
tests/testthat/test_distance.R
tests/testthat/test_generate.R
tests/testthat/test_laplacian.R
tests/testthat/test_plot.R
tests/testthat/test_sigma.R
tests/testthat/test_state.R
vignettes/.gitignore
vignettes/plots_directed.Rmd
vignettes/plots_directed.html
vignettes/plots_directed.html.asis
vignettes/simulate_expression.Rmd
vignettes/simulate_expression.html
vignettes/simulate_expression.html.asis
