diff --git a/.Rbuildignore b/.Rbuildignore old mode 100644 new mode 100755 index 892071b..af5f251 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,3 @@ ^GeneTrajectory\.Rproj$ ^\.Rproj\.user$ +^README\.Rmd$ diff --git a/.Rhistory b/.Rhistory old mode 100644 new mode 100755 diff --git a/.gitignore b/.gitignore old mode 100644 new mode 100755 index cd67eac..e67f93b --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ .Rproj.user +inst/doc diff --git a/DESCRIPTION b/DESCRIPTION index be4faf8..2729611 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,3 +30,7 @@ Imports: biclust, stats, Matrix (>= 1.5) +Suggests: + knitr, + rmarkdown +VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index 974bbe0..b00070a 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,13 +8,11 @@ export(GetGenePseudoorder) export(GetGraphDistance) export(LoadGeneDistMat) export(RunDM) -export(checkIgtPythonEnvironment) export(coarse.grain) export(diffusion.map) export(get.RW.matrix) -export(setupIgtPythonEnvironment) -export(simulate.bifurcation) -export(simulate.coral) -export(simulate.cyclic) -export(simulate.cylinder) -export(simulate.linear) +export(simulate_bifurcation) +export(simulate_coral) +export(simulate_cyclic) +export(simulate_cylinder) +export(simulate_linear) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..a4fe838 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# GeneTrajectory 1.0.0 + +* Initial CRAN submission. diff --git a/R/checkIgtPythonEnvironment.R b/R/checkIgtPythonEnvironment.R deleted file mode 100755 index a4fbbbf..0000000 --- a/R/checkIgtPythonEnvironment.R +++ /dev/null @@ -1,22 +0,0 @@ -#' Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R -#' -#' @export -#' - -checkIgtPythonEnvironment <- function(python.packages = c('ot', 'tqdm', 'scipy.io'), check.numpy=TRUE){ - if(!reticulate::py_available()){ - setupIgtPythonEnvironment() - reticulate::py_available(initialize=TRUE) - } - if(!reticulate::py_available()){ - stop('Python not available. Please install Python, e.g. by using using reticulate::install_python()') - } - if(check.numpy & ! reticulate::py_numpy_available()){ - stop(sprintf('Package "numpy" not available.')) - } - for (p in python.packages) { - if(! reticulate::py_module_available(p)){ - stop(sprintf('Package "%s" not available.', p)) - } - } -} \ No newline at end of file diff --git a/R/setupIgtPythonEnvironment.R b/R/setupIgtPythonEnvironment.R deleted file mode 100755 index 8135347..0000000 --- a/R/setupIgtPythonEnvironment.R +++ /dev/null @@ -1,43 +0,0 @@ -#' Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R -#' -#' @export -#' - -setupIgtPythonEnvironment <- function(condaenv='igt', - virtualenv='igt', - packages=c('numpy', 'scipy', 'pot', 'tqdm'), - create=FALSE){ - if(reticulate::py_available()){ - message(paste('Already set up to ', reticulate::py_exe())) - return(TRUE) - } - - if(reticulate::condaenv_exists(condaenv)){ - message(paste('Using conda environment', condaenv)) - reticulate::use_condaenv(condaenv = condaenv) - return(TRUE) - } - - if(reticulate::virtualenv_exists(virtualenv)){ - message(paste('Using virtualenv environment', condaenv)) - reticulate::use_virtualenv(virtualenv=virtualenv) - return(TRUE) - } - - - if(create & ! reticulate::condaenv_exists(condaenv)){ - reticulate::conda_create(condaenv, packages = packages) - reticulate::use_condaenv(condaenv = condaenv) - return(TRUE) - } - - if(create & ! reticulate::virtualenv_exists(virtualenv)){ - virtualenv_create(virtualenv, packages=packages) - reticulate::use_virtualenv(virtualenv=virtualenv) - return(TRUE) - } - - return(FALSE) -} - - diff --git a/R/simulate.bifurcation.R b/R/simulate_bifurcation.R similarity index 97% rename from R/simulate.bifurcation.R rename to R/simulate_bifurcation.R index 01e101c..a24485e 100755 --- a/R/simulate.bifurcation.R +++ b/R/simulate_bifurcation.R @@ -15,12 +15,12 @@ #' @return #' Returns a gene-by-cell count matrix #' -#' @export simulate.bifurcation +#' @export simulate_bifurcation #' #' @examples #' -simulate.bifurcation <- function(N_cells = 5*c(100, 50, 50), +simulate_bifurcation <- function(N_cells = 5*c(100, 50, 50), N_genes = 5*c(100, 50, 50), model = "poisson", meanlog = 0, diff --git a/R/simulate.coral.R b/R/simulate_coral.R similarity index 97% rename from R/simulate.coral.R rename to R/simulate_coral.R index 1d9cd11..3ec4b4a 100755 --- a/R/simulate.coral.R +++ b/R/simulate_coral.R @@ -16,13 +16,13 @@ #' @return #' Returns a gene-by-cell count matrix #' -#' @export simulate.coral +#' @export simulate_coral #' #' @examples #' -simulate.coral <- function(N_cells = 15*rep(100, 7), +simulate_coral <- function(N_cells = 15*rep(100, 7), N_genes = 2*rep(100, 7), N_genes_CC = 400, model = "poisson", @@ -124,7 +124,7 @@ simulate.coral <- function(N_cells = 15*rep(100, 7), gc_mat_tree <- gc_mat - gc_mat_cyclic <- simulate.cyclic(N_cells = sum(N_cells), + gc_mat_cyclic <- simulate_cyclic(N_cells = sum(N_cells), N_genes = N_genes_CC, model = model, meanlog = meanlog, diff --git a/R/simulate.cyclic.R b/R/simulate_cyclic.R similarity index 97% rename from R/simulate.cyclic.R rename to R/simulate_cyclic.R index bdd43f0..e03fffd 100755 --- a/R/simulate.cyclic.R +++ b/R/simulate_cyclic.R @@ -14,12 +14,12 @@ #' @return #' Returns a gene-by-cell count matrix #' -#' @export simulate.cyclic +#' @export simulate_cyclic #' #' @examples #' -simulate.cyclic <- function(N_cells = 1000, +simulate_cyclic <- function(N_cells = 1000, N_genes = 500, model = "poisson", meanlog = 0, diff --git a/R/simulate.cylinder.R b/R/simulate_cylinder.R similarity index 93% rename from R/simulate.cylinder.R rename to R/simulate_cylinder.R index 7556dec..49911c2 100755 --- a/R/simulate.cylinder.R +++ b/R/simulate_cylinder.R @@ -15,12 +15,12 @@ #' @return #' Returns a gene-by-cell count matrix #' -#' @export simulate.cylinder +#' @export simulate_cylinder #' #' @examples #' -simulate.cylinder <- function(N_cells = 5000, +simulate_cylinder <- function(N_cells = 5000, N_genes = rep(500,2), model = "poisson", meanlog = 0, @@ -31,7 +31,7 @@ simulate.cylinder <- function(N_cells = 5000, sort = TRUE, sparsity = 0.1, theta = 10){ - gc_mat_linear <- simulate.linear(N_cells = N_cells, + gc_mat_linear <- simulate_linear(N_cells = N_cells, N_genes = N_genes[1], model = model, meanlog = meanlog, @@ -42,7 +42,7 @@ simulate.cylinder <- function(N_cells = 5000, sort = sort, sparsity = sparsity, theta = theta) - gc_mat_cyclic <- simulate.cyclic(N_cells = N_cells, + gc_mat_cyclic <- simulate_cyclic(N_cells = N_cells, N_genes = N_genes[2], model = model, meanlog = meanlog, diff --git a/R/simulate.linear.R b/R/simulate_linear.R similarity index 97% rename from R/simulate.linear.R rename to R/simulate_linear.R index ddab476..7af83ee 100755 --- a/R/simulate.linear.R +++ b/R/simulate_linear.R @@ -15,13 +15,13 @@ #' @return #' Returns a gene-by-cell count matrix #' -#' @export simulate.linear +#' @export simulate_linear #' #' @examples #' #' -simulate.linear <- function(N_cells = 1000, +simulate_linear <- function(N_cells = 1000, N_genes = 200, model = "poisson", meanlog = 0, diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000..1851123 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,54 @@ +--- +output: github_document +--- + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/README-", + out.width = "100%" +) +``` + +# GeneTrajectory + + + + +The goal of GeneTrajectory is to ... + +## Installation + +You can install the development version of GeneTrajectory like so: + +``` r +# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE? +``` + +## Example + +This is a basic example which shows you how to solve a common problem: + +```{r example} +library(GeneTrajectory) +## basic example code +``` + +What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: + +```{r cars} +summary(cars) +``` + +You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. + +You can also embed plots, for example: + +```{r pressure, echo = FALSE} +plot(pressure) +``` + +In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN. diff --git a/docs/404.html b/docs/404.html index a32b703..5b0e0cb 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,6 +43,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/articles/GeneTrajectory.html b/docs/articles/GeneTrajectory.html index a4a9c81..cc16fc4 100644 --- a/docs/articles/GeneTrajectory.html +++ b/docs/articles/GeneTrajectory.html @@ -44,6 +44,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/articles/index.html b/docs/articles/index.html index a916af5..5f36afc 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/authors.html b/docs/authors.html index 8af7355..ec53cce 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/index.html b/docs/index.html index a34ed17..68f363d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -44,6 +44,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/checkIgtPythonEnvironment.html b/docs/news/index.html similarity index 67% rename from docs/reference/checkIgtPythonEnvironment.html rename to docs/news/index.html index b731adc..20bb36c 100644 --- a/docs/reference/checkIgtPythonEnvironment.html +++ b/docs/news/index.html @@ -1,11 +1,11 @@ -Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R — checkIgtPythonEnvironment • GeneTrajectoryChangelog • GeneTrajectory -
    +
    -

    Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    - - -
    - -
    -

    Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    -
    - -
    - 
    checkIgtPythonEnvironment(
-  python.packages = c("ot", "tqdm", "scipy.io"),
-  check.numpy = TRUE
-)
    +

    Changelog

    +
    - +
    +

    GeneTrajectory 1.0.0

    +
    • Initial CRAN submission.
      • +
    + +
    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 8ebf6f2..c883d07 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: GeneTrajectory: GeneTrajectory.html -last_built: 2024-04-04T08:48Z +last_built: 2024-04-05T03:46Z diff --git a/docs/reference/AddGeneBinScore.html b/docs/reference/AddGeneBinScore.html index c4fc6fc..7590ac6 100644 --- a/docs/reference/AddGeneBinScore.html +++ b/docs/reference/AddGeneBinScore.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/CoarseGrain.html b/docs/reference/CoarseGrain.html index 2cb3155..224467c 100644 --- a/docs/reference/CoarseGrain.html +++ b/docs/reference/CoarseGrain.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/ExtractGeneTrajectory.html b/docs/reference/ExtractGeneTrajectory.html index 609ee5e..24cc5a8 100644 --- a/docs/reference/ExtractGeneTrajectory.html +++ b/docs/reference/ExtractGeneTrajectory.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/GetGeneEmbedding.html b/docs/reference/GetGeneEmbedding.html index 6723ec2..1e6e518 100644 --- a/docs/reference/GetGeneEmbedding.html +++ b/docs/reference/GetGeneEmbedding.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/GetGenePseudoorder.html b/docs/reference/GetGenePseudoorder.html index 1436479..3923200 100644 --- a/docs/reference/GetGenePseudoorder.html +++ b/docs/reference/GetGenePseudoorder.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/GetGraphDistance.html b/docs/reference/GetGraphDistance.html index a318e17..f25a1bc 100644 --- a/docs/reference/GetGraphDistance.html +++ b/docs/reference/GetGraphDistance.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/LoadGeneDistMat.html b/docs/reference/LoadGeneDistMat.html index 37f421f..225e82c 100644 --- a/docs/reference/LoadGeneDistMat.html +++ b/docs/reference/LoadGeneDistMat.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/RunDM.html b/docs/reference/RunDM.html index 50583ef..ca8da6d 100644 --- a/docs/reference/RunDM.html +++ b/docs/reference/RunDM.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/coarse.grain.html b/docs/reference/coarse.grain.html index c9f0d25..39c8e13 100644 --- a/docs/reference/coarse.grain.html +++ b/docs/reference/coarse.grain.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/diffusion.map.html b/docs/reference/diffusion.map.html index bfde2d5..5f8d8dd 100644 --- a/docs/reference/diffusion.map.html +++ b/docs/reference/diffusion.map.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/get.RW.matrix.html b/docs/reference/get.RW.matrix.html index 9e6aece..c06488a 100644 --- a/docs/reference/get.RW.matrix.html +++ b/docs/reference/get.RW.matrix.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 2d363c7..994f6a1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • @@ -76,10 +79,6 @@

    All functions RunDM()

    Run Diffusion Map on a Seurat object

    - -

    checkIgtPythonEnvironment()

    - -

    Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    coarse.grain()

    @@ -93,27 +92,23 @@

    All functions

    Convert a distance matrix into a random-walk matrix based on adaptive Gaussian kernel

    -

    setupIgtPythonEnvironment()

    - -

    Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    - -

    simulate(<bifurcation>)

    +

    simulate_bifurcation()

    Simulate bifurcating gene process

    -

    simulate(<coral>)

    +

    simulate_coral()

    Simulate a multi-level lineage differentiation process coupled with cell cycle

    -

    simulate(<cyclic>)

    +

    simulate_cyclic()

    Simulate cyclic gene process

    -

    simulate(<cylinder>)

    +

    simulate_cylinder()

    Simulate concurrent independent linear and cyclic gene processes

    -

    simulate(<linear>)

    +

    simulate_linear()

    Simulate linear gene process

    diff --git a/docs/reference/setupIgtPythonEnvironment.html b/docs/reference/setupIgtPythonEnvironment.html deleted file mode 100644 index 7f012a8..0000000 --- a/docs/reference/setupIgtPythonEnvironment.html +++ /dev/null @@ -1,82 +0,0 @@ - -Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R — setupIgtPythonEnvironment • GeneTrajectory - - -
    -
    - - - -
    -
    -
    -

    Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    - - -
    - -
    -

    Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R

    -
    - -
    - 
    setupIgtPythonEnvironment(
-  condaenv = "igt",
-  virtualenv = "igt",
-  packages = c("numpy", "scipy", "pot", "tqdm"),
-  create = FALSE
-)
    -
    - - -
    - -
    - - -
    -

    Developed by Rihao Qu, Francesco Strino.

    -
    - -
    -

    Site built with pkgdown 2.0.7.

    -
    - -
    - - - - - - - - diff --git a/docs/reference/simulate.bifurcation.html b/docs/reference/simulate_bifurcation.html similarity index 94% rename from docs/reference/simulate.bifurcation.html rename to docs/reference/simulate_bifurcation.html index 4f9d5fe..93982cd 100644 --- a/docs/reference/simulate.bifurcation.html +++ b/docs/reference/simulate_bifurcation.html @@ -1,5 +1,5 @@ -Simulate bifurcating gene process — simulate.bifurcation • GeneTrajectorySimulate bifurcating gene process — simulate_bifurcation • GeneTrajectory @@ -27,6 +27,9 @@
  • Reference +
    • +
  • + Changelog
    • @@ -39,7 +42,7 @@

    Simulate bifurcating gene process

    - +
    @@ -47,8 +50,7 @@

    Simulate bifurcating gene process

    - 
    # S3 method for bifurcation
-simulate(
+    
    simulate_bifurcation(
   N_cells = 5 * c(100, 50, 50),
   N_genes = 5 * c(100, 50, 50),
   model = "poisson",
diff --git a/docs/reference/simulate.coral.html b/docs/reference/simulate_coral.html
similarity index 95%
rename from docs/reference/simulate.coral.html
rename to docs/reference/simulate_coral.html
index f171f82..81e9233 100644
--- a/docs/reference/simulate.coral.html
+++ b/docs/reference/simulate_coral.html
@@ -1,5 +1,5 @@
 
-Simulate a multi-level lineage differentiation process coupled with cell cycle — simulate.coral • GeneTrajectorySimulate a multi-level lineage differentiation process coupled with cell cycle — simulate_coral • GeneTrajectory
@@ -27,6 +27,9 @@
 
 
  • 
   Reference
+
    • 
+
  • 
+  Changelog
 
    •
      @@ -39,7 +42,7 @@

      Simulate a multi-level lineage differentiation process coupled with cell cycle

      - +
      @@ -47,8 +50,7 @@

      Simulate a multi-level lineage differentiation process coupled with cell cyc

      - 
      # S3 method for coral
-simulate(
+    
      simulate_coral(
   N_cells = 15 * rep(100, 7),
   N_genes = 2 * rep(100, 7),
   N_genes_CC = 400,
diff --git a/docs/reference/simulate.cyclic.html b/docs/reference/simulate_cyclic.html
similarity index 94%
rename from docs/reference/simulate.cyclic.html
rename to docs/reference/simulate_cyclic.html
index 0abdfbb..4376614 100644
--- a/docs/reference/simulate.cyclic.html
+++ b/docs/reference/simulate_cyclic.html
@@ -1,5 +1,5 @@
 
-Simulate cyclic gene process — simulate.cyclic • GeneTrajectorySimulate cyclic gene process — simulate_cyclic • GeneTrajectory
@@ -27,6 +27,9 @@
 
 
    • 
   Reference
+
      • 
+
    • 
+  Changelog
 
      •
        @@ -39,7 +42,7 @@

        Simulate cyclic gene process

        - +
        @@ -47,8 +50,7 @@

        Simulate cyclic gene process

        - 
        # S3 method for cyclic
-simulate(
+    
        simulate_cyclic(
   N_cells = 1000,
   N_genes = 500,
   model = "poisson",
diff --git a/docs/reference/simulate.cylinder.html b/docs/reference/simulate_cylinder.html
similarity index 94%
rename from docs/reference/simulate.cylinder.html
rename to docs/reference/simulate_cylinder.html
index c9d8cd9..78ad922 100644
--- a/docs/reference/simulate.cylinder.html
+++ b/docs/reference/simulate_cylinder.html
@@ -1,5 +1,5 @@
 
-Simulate concurrent independent linear and cyclic gene processes — simulate.cylinder • GeneTrajectorySimulate concurrent independent linear and cyclic gene processes — simulate_cylinder • GeneTrajectory
@@ -27,6 +27,9 @@
 
 
      • 
   Reference
+
        • 
+
      • 
+  Changelog
 
        •
          @@ -39,7 +42,7 @@

          Simulate concurrent independent linear and cyclic gene processes

          - +
          @@ -47,8 +50,7 @@

          Simulate concurrent independent linear and cyclic gene processes

          - 
          # S3 method for cylinder
-simulate(
+    
          simulate_cylinder(
   N_cells = 5000,
   N_genes = rep(500, 2),
   model = "poisson",
diff --git a/docs/reference/simulate.linear.html b/docs/reference/simulate_linear.html
similarity index 94%
rename from docs/reference/simulate.linear.html
rename to docs/reference/simulate_linear.html
index 97cf25a..a81b7ea 100644
--- a/docs/reference/simulate.linear.html
+++ b/docs/reference/simulate_linear.html
@@ -1,5 +1,5 @@
 
-Simulate linear gene process — simulate.linear • GeneTrajectorySimulate linear gene process — simulate_linear • GeneTrajectory
@@ -27,6 +27,9 @@
 
 
        • 
   Reference
+
          • 
+
        • 
+  Changelog
 
          •
            @@ -39,7 +42,7 @@

            Simulate linear gene process

            - +
            @@ -47,8 +50,7 @@

            Simulate linear gene process

            - 
            # S3 method for linear
-simulate(
+    
            simulate_linear(
   N_cells = 1000,
   N_genes = 200,
   model = "poisson",
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index a34d411..2752e1e 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -15,6 +15,9 @@
   
     /index.html
   
+  
+    /news/index.html
+  
   
     /reference/AddGeneBinScore.html
   
@@ -39,9 +42,6 @@
   
     /reference/RunDM.html
   
-  
-    /reference/checkIgtPythonEnvironment.html
-  
   
     /reference/coarse.grain.html
   
@@ -55,21 +55,18 @@
     /reference/index.html
   
   
-    /reference/setupIgtPythonEnvironment.html
-  
-  
-    /reference/simulate.bifurcation.html
+    /reference/simulate_bifurcation.html
   
   
-    /reference/simulate.coral.html
+    /reference/simulate_coral.html
   
   
-    /reference/simulate.cyclic.html
+    /reference/simulate_cyclic.html
   
   
-    /reference/simulate.cylinder.html
+    /reference/simulate_cylinder.html
   
   
-    /reference/simulate.linear.html
+    /reference/simulate_linear.html
   
 
diff --git a/man/checkIgtPythonEnvironment.Rd b/man/checkIgtPythonEnvironment.Rd
deleted file mode 100644
index f491359..0000000
--- a/man/checkIgtPythonEnvironment.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/checkIgtPythonEnvironment.R
-\name{checkIgtPythonEnvironment}
-\alias{checkIgtPythonEnvironment}
-\title{Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R}
-\usage{
-checkIgtPythonEnvironment(
-  python.packages = c("ot", "tqdm", "scipy.io"),
-  check.numpy = TRUE
-)
-}
-\description{
-Check the Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R
-}
diff --git a/man/setupIgtPythonEnvironment.Rd b/man/setupIgtPythonEnvironment.Rd
deleted file mode 100644
index ae5e481..0000000
--- a/man/setupIgtPythonEnvironment.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/setupIgtPythonEnvironment.R
-\name{setupIgtPythonEnvironment}
-\alias{setupIgtPythonEnvironment}
-\title{Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R}
-\usage{
-setupIgtPythonEnvironment(
-  condaenv = "igt",
-  virtualenv = "igt",
-  packages = c("numpy", "scipy", "pot", "tqdm"),
-  create = FALSE
-)
-}
-\description{
-Set up Python environment for running IGT (Inference of Gene Trajectories) using reticulate package in R
-}
diff --git a/man/simulate.bifurcation.Rd b/man/simulate_bifurcation.Rd
similarity index 88%
rename from man/simulate.bifurcation.Rd
rename to man/simulate_bifurcation.Rd
index 2d98d73..5e8e26a 100644
--- a/man/simulate.bifurcation.Rd
+++ b/man/simulate_bifurcation.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.bifurcation.R
-\name{simulate.bifurcation}
-\alias{simulate.bifurcation}
+% Please edit documentation in R/simulate_bifurcation.R
+\name{simulate_bifurcation}
+\alias{simulate_bifurcation}
 \title{Simulate bifurcating gene process}
 \usage{
-\method{simulate}{bifurcation}(
+simulate_bifurcation(
   N_cells = 5 * c(100, 50, 50),
   N_genes = 5 * c(100, 50, 50),
   model = "poisson",
diff --git a/man/simulate.coral.Rd b/man/simulate_coral.Rd
similarity index 91%
rename from man/simulate.coral.Rd
rename to man/simulate_coral.Rd
index f28ee2d..e3d03d1 100644
--- a/man/simulate.coral.Rd
+++ b/man/simulate_coral.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.coral.R
-\name{simulate.coral}
-\alias{simulate.coral}
+% Please edit documentation in R/simulate_coral.R
+\name{simulate_coral}
+\alias{simulate_coral}
 \title{Simulate a multi-level lineage differentiation process coupled with cell cycle}
 \usage{
-\method{simulate}{coral}(
+simulate_coral(
   N_cells = 15 * rep(100, 7),
   N_genes = 2 * rep(100, 7),
   N_genes_CC = 400,
diff --git a/man/simulate.cyclic.Rd b/man/simulate_cyclic.Rd
similarity index 87%
rename from man/simulate.cyclic.Rd
rename to man/simulate_cyclic.Rd
index 6cb2d0b..477cce1 100644
--- a/man/simulate.cyclic.Rd
+++ b/man/simulate_cyclic.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.cyclic.R
-\name{simulate.cyclic}
-\alias{simulate.cyclic}
+% Please edit documentation in R/simulate_cyclic.R
+\name{simulate_cyclic}
+\alias{simulate_cyclic}
 \title{Simulate cyclic gene process}
 \usage{
-\method{simulate}{cyclic}(
+simulate_cyclic(
   N_cells = 1000,
   N_genes = 500,
   model = "poisson",
diff --git a/man/simulate.cylinder.Rd b/man/simulate_cylinder.Rd
similarity index 89%
rename from man/simulate.cylinder.Rd
rename to man/simulate_cylinder.Rd
index d01d644..2a53bb8 100644
--- a/man/simulate.cylinder.Rd
+++ b/man/simulate_cylinder.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.cylinder.R
-\name{simulate.cylinder}
-\alias{simulate.cylinder}
+% Please edit documentation in R/simulate_cylinder.R
+\name{simulate_cylinder}
+\alias{simulate_cylinder}
 \title{Simulate concurrent independent linear and cyclic gene processes}
 \usage{
-\method{simulate}{cylinder}(
+simulate_cylinder(
   N_cells = 5000,
   N_genes = rep(500, 2),
   model = "poisson",
diff --git a/man/simulate.linear.Rd b/man/simulate_linear.Rd
similarity index 88%
rename from man/simulate.linear.Rd
rename to man/simulate_linear.Rd
index 5a218d3..a00aebb 100644
--- a/man/simulate.linear.Rd
+++ b/man/simulate_linear.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulate.linear.R
-\name{simulate.linear}
-\alias{simulate.linear}
+% Please edit documentation in R/simulate_linear.R
+\name{simulate_linear}
+\alias{simulate_linear}
 \title{Simulate linear gene process}
 \usage{
-\method{simulate}{linear}(
+simulate_linear(
   N_cells = 1000,
   N_genes = 200,
   model = "poisson",