manual update.

vignettes/about.Rmd

@@ -7,15 +7,19 @@ output: html_document
 
 * This program is developed based on the Shiny framework, a set of R packages and a collection of scripts written by members of Junhyong Kim Lab at University of Pennsylvania. Its goal is to facilitate fast and interactive RNA-Seq data analysis and visualization. 
 
-* You may not use this file except in compliance with the Kim Lab License located at
-
-     http://kim.bio.upenn.edu/software/LICENSE
-
- Unless required by applicable law or agreed to in writing, this
- software is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
- CONDITIONS OF ANY KIND, either express or implied.  See the License
- for the specific language governing permissions and limitations
- under the License.
+* This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
 * Script Contributors:
 

vignettes/manual_file.Rmd

@@ -28,7 +28,8 @@ See http://kim.bio.upenn.edu/software/pivot.shtml for more details.
 
 ```
 # dependecies that needs to be manually installed 
-install.packages("devtools") # First run this line alone then paste rest.
+# Copy the following line by line.
+install.packages("devtools") 
 library("devtools")
 source("http://bioconductor.org/biocLite.R")  
 biocLite("GO.db")
@@ -59,38 +60,6 @@ library(PIVOT)
 pivot()
 ```
 
-* For advanced users, if you want to only load needed modules,
-
-Then you can either use 
-```
-pivot_module()
-```
-which shows the available modules in PIVOT:
-
-|ID|Module|
-|---|---|
-|1|PIVOT.base|
-|2|DESeq2|
-|3|edgeR|
-|4|scde|
-|5|monocle|
-|6|PIVOT.network|
-|7|caret|
-|8|PIVOT.toolkit|
-
-Then use `pivot(#ID_vector)` to launch selected modules, e.g., pivot(c(1,2,3)) to launch PIVOT with the base PIVOT module, DESeq2 and edgeR.
-
-<img src="figures/launcher.png" style= "margin-right: 20px; outline-style: double; outline-color: Gainsboro;" width="70%"/>
-
-Alternatively, use
-```
-pivot_launcher()
-```
-to launch a window to directly pick modules or install required components.
-
-
-<p style="clear:both;">
-
 # Data Input
 
 ## Input expression matrix