KimLabIDV

eagle-i ID

Resource Type

Properties

1. Resource Description

   "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 IDV supports routine RNA-Seq data analysis including DESeq normalization, differential expression analysis, principal component analysis, pairwise correlation, hierarchical/K-means clustering, group classification and plotting of gene heatmap. It also supports report generation and program state sharing. KimLabIDV is provided as an R package and runs as a web application. It has been tested on Mac OSX and Windows."

2. Additional Name

   An Interactive Data Visualization Tool for Single-Cell Gene Expression Analysis

3. Used by

   Kim Laboratory: Computational Evolutionary Biology

4. Version

   1.03

5. Operating System

   Mac OSX

6. Operating System

   Windows

7. Data Input

   Count files

8. Data Output

   Normalized counts

9. Data Output

   Basic data statistics

10. Data Output

    ERCC read distribution

11. Data Output

    Differentially expressed genes

12. Data Output

    Monocle Cell State Ordering

13. Data Output

    Correlation analysis pairwise scatterplot

14. Data Output

    Sample correlation heatmap

15. Data Output

    Feature heatmap

16. Data Output

    Dimension reduction results

17. Data Output

    Classification

18. Data Output

    Report

19. Software purpose

    Gene expression data correction objective

20. Software purpose

    Documentation generation objective

21. Software purpose

    Differential expression analysis objective

22. Software purpose

    Gene expression analysis

23. Software purpose

    Data rendering and visualization objective

24. Website(s)

    http://kim.bio.upenn.edu/software/idv.shtml

25. Related Technique

    Single-cell gene expression assay

26. Related Technique

    RNA sequencing

27. Developed by

    Kim Laboratory: Computational Evolutionary Biology

28. Software license

    Academic software license

29. Coded in

    R language