PANDA-view

What is it?

PANDA-view is developed for statistical analysis and data visualization as an affiliated tool of PANDA. PANDA-view can directly read and perform a multi-level representation of PANDA’s quantification results. In addition, PANDA-view is compatible with other -omics tools by taking their results in tab-delimited text (*.txt) and CSV (*.csv) file formats as input. The core of PANDA-view was written in Qt C++ language on the platform of Microsoft Visual Studio ultimate 2013 under Windows System. And the interface of PANDA-view was implemented in C# on the same platform. Parts of the functions in PANDA-view are developed based on R statistical environment.

Cite PANDA-view

• PANDA-view is published in Bioinformatics on 5/22/2018!

The release version

PANDA-view version v1.1.3 (1/11/2019)

Major update!

(1) For missing value imputation:

• Five minimum imputation methods (i.e. row minimum, column minimum, global minimum, user-defined minimum and random top5% minimum) have been added for missing value imputation.

• The random top5% minimum imputation method is performed as follows:

  1. We firstly use the top5% minimal data to fit a Gaussian distribution.
  2. Then the missing values are imputated by the random values generated from the Gaussian distribution.
  3. To use this method, at least 100 data points are required.
  4. Please note that the random values may be negative.

• Zero value, empty value, invalid value (such as NaN, NULL, na, null) are all cosidered as missing value in PANDA-view.

• Users are allowed to remove the rows containing any missing value in the GUI of Imputation settings.
• For the input file containing negative values, imputation method can be performed by considering zero value as missing value.

(2) For normalization:

• A min-max scaling method has been added which can handle negative values.

$$x_norm=(x-min)/(max-min)$$

(3) For statistical anlysis:

• Pairwise t test has been added in the GUI of ANOVA. For multiple groups, users can perform both ANOVA and pairwise t test.
• For pairwise t test, seven p-value correction methods are provided (abbr. "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr") in the Pairwise parameter setting. And users can also choose not to correct p-value (by selecting "none" in the Pairwise parameter setting).

PANDA-view version v1.1.2 (7/18/2018)

• A bug in R script for clustering function is fixed.

PANDA-view version v1.1.1 (5/24/2018)

• Another required R package "vsn" is added in version 1.1.1 for VSN normalization method.

PANDA-view version v1.1.0 (4/27/2018) (major improvement)

PANDA-view v1.1.0 has several major updates:

• A new function (“R requirement” button in menu) has been added to check if the R environment and all the necessary R packages are successfully configured and installed before using PANDA-view.
• Two normalization methods (Quantile normalization and VSN) have been added.
• The required R packages and their corresponding parameters will be shown in the GUI for every statistical analysis method.
• Figures can be exported as PDF.
• Other refinements in GUI.

PANDA-view version v1.0.4 (1/29/2018)

• PANDA-view v1.0.4 fixed a bug about the "Move Down" button in GUI. This bug did not influence the function of PANDA-view.

PANDA-view version v1.0.3 (12/25/2017)

• PANDA-view v1.0.3 fixed a bug about multiple hypothesis tests.
• The waiting icon was updated.

PANDA-view version v1.0.2 (12/18/2017)

• PANDA-view v1.0.2 fixed a bug when showing statistical results and some typos in GUI.
• PANDA-view can read Chinese files by supporting UTF-8 since v1.0.2! (important)

PANDA-view version v1.0.1 (8/31/2016)

• PANDA-view v1.0.1 fixed a bug when plotting the multiple XICs for precursor-labeled data.

PANDA-view version v1.0.0 (8/1/2016)

• The first release version of PANDA-view.

Hardware requirements

• Intel Pentium III/800 MHz or higher (or compatible) although one should probably not go below a dual core processor.
• 2 GB RAM minimum.

Software requirements

(1) Microsoft Visual C++ Redistributable for Visual Studio 2013

(2) Supported operating system (OS) versions (32-bit or 64-bit)

• Windows Vista SP2
• Windows 7 SP1
• Windows 8
• Windows 10
• Windows Server 2008 R2 SP1
• Windows Server 2008 SP2

(3) .NET Framework 4.5 or higher from Microsoft

(4) R v3.1.0 for Windows or higher from R project

Note1

R software can be downloaded from https://www.r-project.org/. Users should also add the directory which includes RScript.exe (such as "c:\Program Files\R\R-3.3.3\bin\") into the system environment variable. In addition, the path “c:\Program Files\R\R-3.3.3\bin\x64\” should also be added for the 64-bit OS.

The method for setting system environment variable can be found at http://www.computerhope.com/issues/ch000549.htm.

Note2

The required R packages and their installation commands are listed below:

install.packages("rgl")
install.packages("scatterplot3d")
install.packages("RColorBrewer")
install.packages("gplots")
install.packages("survival")
install.packages("coin")
install.packages("Rcpp")
install.packages("lattice")
install.packages("mice")
# With R version 3.4 or lower: 
source("http://bioconductor.org/biocLite.R")
biocLite("Biobase") 
biocLite("limma")
biocLite("vsn")
biocLite("impute")
biocLite("R.methodsS3")
biocLite("matrixStats")
biocLite("samr")
# With R version 3.5 or greater: 
install.packages("BiocManager") 
BiocManager::install("Biobase") 
BiocManager::install("limma") 
BiocManager::install("vsn") 
BiocManager::install("impute") 
BiocManager::install("R.methodsS3") 
BiocManager::install("matrixStats") 
BiocManager::install("samr")

Installation

Download link: https://sourceforge.net/projects/panda-view/

Please see User Manual for PANDA-view.pdf and PANDA-view_ConfigurationVideo.avi for details.

License

Please see the file called LICENSE_English.pdf or LICENSE_Chinese.pdf.

Contact

For any questions involving PANDA and PANDA-view, please contact Dr. Cheng Chang (Email: changchengbio@163.com).

Copyright

This software product is developed by Dr. Cheng Chang from the National Center for Protein Sciences (Beijing)-Bioinformatics group. All title and intellectual property rights, which is generated by the software product (including, but not limited to, relative images, data, texts, additional program and other software products (dll, exe, etc.), incidental help materials, and any copies of the Software Products are protected by Copyright Law of People’s Republic of China and international copyright treaties and other intellectual property laws and treaties. Users only get the right to use this software product.