Recent changes to Home

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Wed, 10 Jul 2019 15:41:27 -0000

--- v10
+++ v11
@@ -56,7 +56,7 @@
 library(MoPAC)
 run.MoPAC()

-Instructions are provided within the interface. A video tutorial is also underway.
+Instructions are provided within the interface. A video tutorial is shown below:

 [[embed url=https://www.youtube.com/watch?v=D2Wd-ON69QQ]]

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Wed, 10 Jul 2019 15:40:42 -0000

--- v9
+++ v10
@@ -58,6 +58,8 @@

 Instructions are provided within the interface. A video tutorial is also underway.

+[[embed url=https://www.youtube.com/watch?v=D2Wd-ON69QQ]]
+
 For any questions please email <odvillarreal@mdanderson.org> or <oscardvillarreal@gmail.com>.

 # Download
</oscardvillarreal@gmail.com></odvillarreal@mdanderson.org>

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Fri, 07 Jun 2019 10:25:10 -0000

--- v8
+++ v9
@@ -66,6 +66,23 @@

 [[download_button]]

+# Version history
+
+#### 0.3.1
+
+Added a sample sgRNA library file to be used in the upcoming tutorial.
+
+#### 0.3.0
+
+Source code using the new methodology.
+
+#### 0.2.0
+
+Improved interface and bug fixes for the method used in the Gao et al. publication.
+
+#### 0.1.0
+
+Source code of the method originally used in the Gao et al. publication.

 [[members limit=20]]

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Fri, 07 Jun 2019 09:59:05 -0000

--- v7
+++ v8
@@ -2,7 +2,7 @@

 MoPAC is an R package which may be installed through the following command in a terminal running R or in the Rstudio console:

-install.packages("MoPAC_0.3.0.tar.gz",repos=NULL,type="source")
+install.packages("MoPAC_0.3.1.tar.gz",repos=NULL,type="source")

 It might take over a minute to install due to the large size of the STRING gene interaction dataset.

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 21:33:35 -0000

--- v6
+++ v7
@@ -6,7 +6,7 @@

 It might take over a minute to install due to the large size of the STRING gene interaction dataset.

-### Dependencies:
+###### Dependencies:

 Several R packages must be installed beforehand for the installation to be successfull:

@@ -35,7 +35,7 @@
 install.packages("neat")
 install.packages("igraph")

-### Optional dependencies:
+###### Optional dependencies:

 The "STRINGdb" R package is optional but highly recommended for enhanced visualization of gene interaction networks:

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 21:32:53 -0000

--- v5
+++ v6
@@ -4,7 +4,11 @@

 install.packages("MoPAC_0.3.0.tar.gz",repos=NULL,type="source")

-Several other R packages must be installed beforehand for the installation to be successfull:
+It might take over a minute to install due to the large size of the STRING gene interaction dataset.
+
+### Dependencies:
+
+Several R packages must be installed beforehand for the installation to be successfull:

 install.packages("Rcpp")
 install.packages("gtools")
@@ -31,6 +35,8 @@
 install.packages("neat")
 install.packages("igraph")

+### Optional dependencies:
+
 The "STRINGdb" R package is optional but highly recommended for enhanced visualization of gene interaction networks:

 source("https://bioconductor.org/biocLite.R")
@@ -43,8 +49,6 @@
 sudo yum install libcurl-devel
 sudo yum install pandoc
 install.packages("plotly")
-
-It might take over a minute to install due to the large size of the STRING gene interaction dataset.

 # Usage
 Once installed, the interactive user interface may be started through the following two commands in a terminal running R or in the Rstudio console:

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 19:57:16 -0000

--- v4
+++ v5
@@ -52,6 +52,8 @@
 library(MoPAC)
 run.MoPAC()

+Instructions are provided within the interface. A video tutorial is also underway.
+
 For any questions please email <odvillarreal@mdanderson.org> or <oscardvillarreal@gmail.com>.

 # Download
</oscardvillarreal@gmail.com></odvillarreal@mdanderson.org>

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 19:26:22 -0000

--- v3
+++ v4
@@ -1,5 +1,58 @@
 # Installation

+MoPAC is an R package which may be installed through the following command in a terminal running R or in the Rstudio console:
+
+install.packages("MoPAC_0.3.0.tar.gz",repos=NULL,type="source")
+
+Several other R packages must be installed beforehand for the installation to be successfull:
+
+install.packages("Rcpp")
+install.packages("gtools")
+install.packages("stringr")
+install.packages("openxlsx")
+install.packages("tensorA")
+install.packages("ineq")
+install.packages("reshape2")
+install.packages("plyr")
+install.packages("ggplot2")
+install.packages("gplots")
+install.packages("ggrepel")
+install.packages("gridExtra")
+install.packages("knitr")
+install.packages("rmarkdown")
+install.packages("shiny")
+install.packages("shinyBS")
+install.packages("shinythemes")
+install.packages("shinyFiles")
+install.packages("DT")
+install.packages("visNetwork")
+install.packages("sqldf")
+install.packages("rhandsontable")
+install.packages("neat")
+install.packages("igraph")
+
+The "STRINGdb" R package is optional but highly recommended for enhanced visualization of gene interaction networks:
+
+source("https://bioconductor.org/biocLite.R")
+biocLite("STRINGdb")
+
+If you wish to generate pdf and html reports, which is an optional feature, additional distribution-specific installations are necessary, for example in Fedora/RedHat/CentOS:
+
+sudo yum install libpng-devel
+sudo yum install openssl-devel
+sudo yum install libcurl-devel
+sudo yum install pandoc
+install.packages("plotly")
+
+It might take over a minute to install due to the large size of the STRING gene interaction dataset.
+
+# Usage
+Once installed, the interactive user interface may be started through the following two commands in a terminal running R or in the Rstudio console:
+
+library(MoPAC)
+run.MoPAC()
+
+For any questions please email <odvillarreal@mdanderson.org> or <oscardvillarreal@gmail.com>.

 # Download

</oscardvillarreal@gmail.com></odvillarreal@mdanderson.org>

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 18:57:53 -0000

--- v2
+++ v3
@@ -1,11 +1,12 @@
-Welcome to your wiki!
+# Installation

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

-The wiki uses [Markdown](/p/mopac/wiki/markdown_syntax/) syntax.
-
-[[members limit=20]]
+# Download

 The latest version of MoPAC (0.3) is available here:

 [[download_button]]
+
+
+[[members limit=20]]
+

Home modified by Oscar David Villarreal Escamilla

Oscar David Villarreal Escamilla — Thu, 06 Jun 2019 18:55:44 -0000

--- v1
+++ v2
@@ -5,4 +5,7 @@
 The wiki uses [Markdown](/p/mopac/wiki/markdown_syntax/) syntax.

 [[members limit=20]]
+
+The latest version of MoPAC (0.3) is available here:
+
 [[download_button]]