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PIVOT

PIVOT: Platform for Interactive analysis and Visualization Of Transcriptomics data

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. Current version of PIVOT supports routine RNA-Seq data analysis including normalization, differential expression analysis, dimension reduction, correlation analysis, clustering and classification. Users can complete workflows of DESeq2, monocle and scde package with just a few button clicks. All analysis reports can be exported, and the program state can be saved, loaded and shared.

PIVOT is provided as an R package and runs as a web application. It supports any system with R and Rstudio installed.

Screen shots...

Manual (zip)

Update Log

• PIVOT v1.0.0 - Changed name from KimLabIDV to PIVOT. Complete re-written of the original package. (Mar 25, 2017)
• KimLabIDV v1.03 - Simplified the installation process. Added mac package with portable library. Added windows version. (Dec 20, 2015)
• KimLabIDV v1.02.1 - Fixed an install script typo. (Dec 16, 2015)
• KimLabIDV v1.02 - First stable release. (Dec 11, 2015)

Installation:

• Main Program: Please copy and paste the following command to R console. Upgrading R and Rstudio to the latest version is strongly recommended.
# dependecies that needs to be manually installed # First run this line alone then paste rest. install.packages("devtools") library("devtools") source("http://bioconductor.org/biocLite.R") biocLite("GO.db") biocLite("HSMMSingleCell") biocLite("org.Mm.eg.db") biocLite("org.Hs.eg.db") biocLite("DESeq2") biocLite("SingleCellExperiment") biocLite("scater") # Install PIVOT install_github("kimpenn/PIVOT") biocLite("BiocGenerics") # You need the latest BiocGenerics >=0.23.3
• (Optional but strongly recommended) Dependencies:
  • For report generation, you need Pandoc: http://pandoc.org/installing.html
  • For PDF report generation, you need Latex: https://www.latex-project.org/get/

Running PIVOT:

• Note you MUST launch PIVOT with Rstudio.
• To run PIVOT, in Rstudio console, use command
library(PIVOT) pivot()

Troubleshooting

• URL 'http://xxx.tgz': status was '404 Not Found'.
  • Call chooseCRANmirror() to select another CRAN mirror.

• Current known bug and workaround:
  • Some times when user press the "launch module" or "clean session" button, new window does not show up. In such cases, please call the last command you see in Rstudio, i.e., pivot_main() or pivot('clean')

Citation