Merge branch 'master' of https://github.com/CityUHK-CompBio/HTSanalyzeR2

README.md

@@ -1,17 +1,76 @@
-# HTSanalyzeR2
-Development version of HTSanalyzeR2
+# HTSanalyzeR2  
 
-## Installation
+Welcome to the homepage of HTSanalyzeR2 package.
 
-```
-# Before installing HTSanalyzeR2, please install Bioconductor first if you've not.
+This package provides gene set over-representation, enrichment and network analyses for various preprocessed high-throughput data as well as corresponding time-series data including CRISPR, RNA-seq, micro-array and RNAi. It could also generate a dynamic shiny report encompassing all the results and visualizations, facilitating the users maximally for downloading, modifying the visualization parts with personal preference and sharing with others by publishing the report to [Shinyapps.io](http://shiny.rstudio.com/articles/shinyapps.html).
+
+## Quick Installation
+
+If you are a current bioconductor user and have `devtools` package installed, you only need to call `install_github` function in `devtools` to install `HTSanalyzeR2`. If you encountered errors, please refer to the section *Potential Dependency Issues*.  
 
+```
+# Installation requires bioconductor and devtools, please use the following commands if you've not
 source("https://bioconductor.org/biocLite.R")
-biocLite()
+biocLite(c("devtools"))
+
+# Then install HTSanalyzeR2
+
+devtools::install_github("CityUHK-CompBio/HTSanalyzeR2", build_vignettes=TRUE, 
+  repos=BiocInstaller::biocinstallRepos(),
+  dependencies=TRUE, type="source")
+```
+
+## Dependency
+
+`HTSanalyzeR2` requires the following R/Bioconductor packages for its full function:    
+
+- GO.db 
+- cellHTS2 
+- Rcpp 
+- foreach 
+- stringr 
+- igraph 
+- BioNet 
+- DT 
+- shiny 
+- shinydashboard 
+- colourpicker 
+- KEGGREST 
+- data.table 
+- htmlwidgets 
+- methods 
+- RankProd 
+- AnnotationDbi 
+- graphics 
+- grDevices 
+- stats 
+- utils 
 
-# Then you need to install the following github installer package and dependent package.
-BiocInstaller::biocLite(c("devtools", "GO.db"))
+`HTSanalyzeR2` also suggests the following R/Bioconductor packages for improved user experience:  
 
-# Install HTSanalyzeR2.
-devtools::install_github("CityUHK-CompBio/HTSanalyzeR2")
+- BiocStyle  
+- rmarkdown  
+- testthat  
+- knitr  
+- org.Hs.eg.db  
+- doParallel  
+- Biobase  
+
+
+#### Potential Dependency Issues
+
+If you are using ubuntu, common dependency issues should be solved using the following one line command:  
 ```
+sudo apt-get install -y libssl-dev libcurl4-openssl-dev libxml2-dev libgmp-dev libmpfr-dev
+```
+
+Details about this:  
+
+1. `devtools` need package `git2r`, which requires openssl library. Please install `libssl-dev` on Ubuntu or corresponding package on other OS.
+
+2. `devtools` need package `httr`, which requires curl library. Please install `libcurl4-openssl-dev` on Ubuntu or corresponding package on other OS.
+
+3. `igraph` requres xml library. Please install `libxml2-dev` on Ubuntu or corresponding package on other OS.
+
+4. `RankProd` need package `Rmpfr`, which requires gmp and mpfr library. Please install `libgmp-dev` and `libmpfr-dev` on Ubuntu or corresponding package on other OS.
+