Updated Readme, Installation guide and some fixes.

CSOgroup · Aug 23, 2024 · 37099d6 · 37099d6
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diff --git a/INSTALLATION.md b/INSTALLATION.md
@@ -8,4 +8,33 @@
 devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
 ```
 
-## Installation with micromamba enviorment
+## Installation with micromamba enviorment
+
+
+`micromamba` is a tiny version of the mamba package manager (Like Conda). Refer [website](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for it's installation guide.
+
+Steps to follow after installing micromamba in a terminal:
+
+`micromamba create -n r_env r-essentials r-base`
+`micromamba activate r_env`
+`micromamba install conda-forge::r-devtools`
+`micromamba install conda-forge::armadillo`
+`micromamba install conda-forge::r-rcppparallel`
+`micromamba install conda-forge::r-rfast`
+
+- After this run R and install `SelectSim` R package as follows
+``` r
+# install.packages("devtools")
+devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
+```
+
+Alternative way install with provided `enviorment.yml` file.
+
+`micromamba create -f env.yml`
+`micromamba activate r_env`
+- After this run R and install `SelectSim` R package as follows
+``` r
+# install.packages("devtools")
+devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
+```
+
diff --git a/README.Rmd b/README.Rmd
@@ -17,8 +17,9 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 <!-- badges: end -->
 
-The goal of SelectSim is to implement the methodology to infer inter-dependencies between functional alterations in cancer.
+The goal of SelectSim package is to implement the methodology to infer inter-dependencies between functional alterations in cancer. SelectSim estimates the expected number of mutations in a given gene and a given sample from the mutation frequency of the gene, f(g), and the tumor mutation burden (TMB) of the sample, $\mu$(t). These values can be estimated within specific mutation and tumor subsets, to account for heterogeneous tumor types, tissue specificities, and distinct mutational processes
 
+![SelectSim Method](SelectSim_method.png)
 
 ## Installation
 
@@ -34,7 +35,7 @@ devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignett
 
 ## Example
 
-Check the the vignettes folder.
+Check the the Vignettes folder or visit [website](https://csogroup.github.io/SelectSim/)
 
 ### Who do I talk to? ###
 

diff --git a/README.md b/README.md
@@ -6,8 +6,19 @@
 <!-- badges: start -->
 <!-- badges: end -->
 
-The goal of SelectSim is to implement the methodology to infer
-inter-dependencies between functional alterations in cancer.
+The goal of SelectSim package is to implement the methodology to infer
+inter-dependencies between functional alterations in cancer. SelectSim
+estimates the expected number of mutations in a given gene and a given
+sample from the mutation frequency of the gene, f(g), and the tumor
+mutation burden (TMB) of the sample, $\mu$(t). These values can be
+estimated within specific mutation and tumor subsets, to account for
+heterogeneous tumor types, tissue specificities, and distinct mutational
+processes
+
+<figure>
+<img src="SelectSim_method.png" alt="SelectSim Method" />
+<figcaption aria-hidden="true">SelectSim Method</figcaption>
+</figure>
 
 ## Installation
 
@@ -24,7 +35,8 @@ devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignett
 
 ## Example
 
-Check the the vignettes folder.
+Check the the Vignettes folder or visit
+[website](https://csogroup.github.io/SelectSim/)
 
 ### Who do I talk to?
 

diff --git a/SelectSim_method.png b/SelectSim_method.png
diff --git a/docs/INSTALLATION.html b/docs/INSTALLATION.html
diff --git a/docs/articles/data_processing.html b/docs/articles/data_processing.html
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   data_processing: data_processing.html
   introduction: introduction.html
-last_built: 2024-08-23T09:02Z
+last_built: 2024-08-23T11:08Z
 urls:
   reference: https://csogroup.github.io/SelectSim/reference
   article: https://csogroup.github.io/SelectSim/articles

diff --git a/docs/search.json b/docs/search.json