Instructions
The app is hosted on the website: https://kcvi.shinyapps.io/START/
+Note, this is version 1.1.1, published on 12/9/19. If you need the previous version, it is hosted here: kcvi.shinyapps.io/STARTapp_2018/
Code can be found on github: https://github.com/jminnier/STARTapp
+Please post issues on github, and feel free to contribute by forking and submitting development branches.
To run this app locally on your machine, download R or RStudio and run the following commands once to set up the environment:
install.packages(c("reshape2","ggplot2","ggthemes","gplots","ggvis","dplyr","tidyr","DT",
"RColorBrewer","pheatmap","shinyBS","plotly","markdown","NMF","scales","heatmaply"))
@@ -163,10 +418,7 @@ Count or Expression Data
- Each row denotes a gene, each column denotes a sample.
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Count data contains read counts for each gene for each sample, along with gene identifiers.
Analysis: When raw counts are uploaded, the data is then analyzed by the app. The app uses the voom method from the ‘limma’ Bioconductor package to transform the raw counts into logged and normalized intensity values. These values are then analyzed via linear regression where gene intensity is regressed on the group factor. P-values from all pairwise regression tests for group effect are computed and Benjamini-Hochberg false discovery rate adjusted p-values are computed for each pairwise comparison. The “log2cpm” values are the log2-counts-per-million values. The “log2cpm_voom” values are the normalized logcpm values from the voom method. Both methods use an offset of 0.5, which means 0.5 is added to all count values before normalizing (in the case of voom) and log transforming so that 0 counts have non infinite values.
Example file: https://github.com/jminnier/STARTapp/blob/master/data/examplecounts_short.csv
@@ -177,10 +429,7 @@ Analyzed Data
Each row denotes a gene, each column denotes a sample.
Additional columns provide Fold Changes and P-values
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Analyzed data must contain some kind of expression measure for each sample (i.e. counts, normalized intensities, CPMs), and a set of p-values with corresponding fold changes for those p-values. For instance, if you have a p-value for the comparison of group1 vs group2, you can upload the observed fold change or log2(fold change) between group1 vs group2. If you have a more complex design and do not have fold changes readily available, you may upload the test statistics or other similar measures of effect size as placeholders. The fold changes are mainly used in the volcano plots. We recommend uploading p-values that are adjusted for multiple comparisons (such as q-values from the qvalue package, or adjusted p-values from p.adjust() function in R).
Example file: https://github.com/jminnier/STARTapp/blob/master/data/exampleanalysisres_short.csv
@@ -188,7 +437,7 @@ Analyzed Data
TIP: Save Data for Future Upload
After submitting a raw data or analyzed file, you may download the .csv file with the analysis results for your own use (or to upload as an “analyzed data”) or more conveniently click the button “Save Results as RData File for Future Upload” so that you may easily and quickly upload your data to the START app in the future under the “RData from previous START upload” option with one click.
-After uploading your data to START, click red button 
+After uploading your data to START, click red button
to download an .RData file to upload your data to START with one click.
Next time use the “Input Data” tab –> “START RData file” option.
@@ -242,18 +491,39 @@ Heatmap
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diff --git a/instructions/Instructions.md b/instructions/Instructions.md
index abed9ad..0350b2b 100644
--- a/instructions/Instructions.md
+++ b/instructions/Instructions.md
@@ -13,8 +13,12 @@ output:
The app is hosted on the website: https://kcvi.shinyapps.io/START/
+*Note, this is version 1.1.1, published on 12/9/19. If you need the previous version, it is hosted here: [kcvi.shinyapps.io/STARTapp_2018/](https://kcvi.shinyapps.io/STARTapp_2018/)*
+
Code can be found on github: https://github.com/jminnier/STARTapp
+Please post [issues on github](https://github.com/jminnier/STARTapp/issues/), and feel free to contribute by forking and submitting development branches.
+
To run this app locally on your machine, download R or RStudio and run the following commands once to set up the environment:
```
diff --git a/instructions/landing.md b/instructions/landing.md
index 785bc1e..b215cd0 100644
--- a/instructions/landing.md
+++ b/instructions/landing.md
@@ -7,6 +7,7 @@ output: html_document
- *Explore* the app's features with the example data set pre-loaded by clicking on the tabs above.
- *Upload* your data in the "Input Data" tab.
+*Note, this is version 1.1.1, published on 12/9/19. If you need the previous version, it is hosted here: [kcvi.shinyapps.io/STARTapp_2018/](https://kcvi.shinyapps.io/STARTapp_2018/)*
#### Features