dbdimitrov / bingleseq Goto Github PK

By mistake. Kindly delete.

I have two questions.

1. Is it possible to load metadata for single cell RNAseq in BingleSeq?

2. I have 10x count data of 49 cells which are fewer than 50. It creates issue when running unsupervised clustering, because default setting is 50 cells. But I cannot change in BingleSeq module.

Warning: Error in irlba: max(nu, nv) must be strictly less than min(nrow(A), ncol(A))

Do you have suggestion?

Thanks,

This error
Warning: Error in show_waiter: could not find function "show_waiter" 73: observeEventHandler 2: runApp 1: startBingleSeq
appears in differential Expression (bulk analysis) when Run DE Analysis even with sample data, Shiny closes instantly

Hi

I encountered a problem when running bulk RNAseq analysis.
Error message is described below:

'show_waiter' is deprecated.
Use 'waiter_show' instead.
See help("Deprecated") and help("waiter-deprecated").

Thank you.

Hello,
Is it possible for you to add some steps describing how to actually launch the GUI? I managed to get everything installed, but can't figure that out.

This is really attractive to someone like me who would like to play around in Seurat, etc. but never finds the time to actually learn R.

Thanks!

Hi,

I want to use BingleSeq for RNASeq data analysis on Mouse genome but it continuously throwing the same error of “Incorrect Gene Type” (Please find the attachment). I tried all the possibility but I am not able to resolve it.

Further, in gene Ontology section, there are two time mm9 genome is mentioned in the “Select Genome” section. What is the explanation behind it?

I am attaching a sample and meta data file for your reference. Your response will be highly appreciated.

design_BingleSeq.txt

Sample_Data.txt

Thanks & Best Regards,

Akhilesh Mishra, Ph.D.

Hi David,

some minor comments I forgot to mention yesterday:

• For the application it would be nice if you could provide some example data within the application (Could be similar to what I have done in the tab Enrichment analysis of this app: https://saezlab.shinyapps.io/reheat/). This would allow interested users and potential reviewers to explore your app in depth without the need to upload own data

• You mixed up the x and y labels of the volcano plot in the README file

• In my opinion It is a better practice to show the unadjusted p-value on the y-axis of the volcano plot. Why? Different p-values could map to the same adjusted p-value, so you loose some distinction/information between different genes. However, as a cutoff for regulation you should still use the corrected p-value

All the best,
Christian

Hi

I encountered an Data format error when running Differential Expression with batch correction, but didn't without the correction process.
The error messages are described below:

警告:  'show_waiter' is deprecated.
Use 'waiter_show' instead.
See help("Deprecated") and help("waiter-deprecated").
 警告:  'hide_waiter' is deprecated.
Use 'waiter_hide' instead.
See help("Deprecated") and help("waiter-deprecated").
 警告:  Error in rownames_to_column: is.data.frame(df) is not TRUE
  113: <Anonymous>

Thank you.