Error message:
Error: ModuleNotFoundError: No module named 'scripts.DigitalCellSorter_interactive'
Detailed traceback:
File "", line 5, in

The method to install BioClite has changed for R version >=6.0.

For the import, we need to remove the gene ID column. So if we directly import from GEO, will the loading automatically remove this column?

For GEO import, there is problem with this data. Once the normalized data is submitted, the message says data imported. The user should move directly to transcriptomics analysis. But if I do that, there is no data available to analyse. If I go to Preprocessing (which I should not since data is already preprocessed), the default RLE is doing circles but no response. Known to be fixed ASAP.

Can you check for entropy whether we are using entropy.empirical with default fixed bin size?
The bin size should not be fixed across all dataset, it has to follow Doan’s rule:
http://msmbuilder.org/mdentropy/0.3.0/generated/mdentropy.core.binning.doanes_rule.html#mdentropy.core.binning.doanes_rule

The formula can be found in methods (Entropy analysis):
https://www.nature.com/articles/srep07137

Also for PCA, when I choose the top 50, or 100, etc. the PCA plots do not change. They remain the same as the whole data. That is, they are not updated for each selection

Currently, it takes around 3 to 4 minutes to load our webserver hosted at http://combio-sifbi.org/ABioTrans/ which can be improved by changing the shiny-server configurations.
Maybe removing the automatic timeout will resolve this issue.

Right now we won't have any Docker container for our software but we will be very happy to have one.

The aim of this issue will be to have a docker container named as abiotrans which any user can pull and run on all of the features offered by our software.

Steps

1. Clone our repo inside the container
2. Install and configure all the dependencies needed.
3. Configure shiny-server
4. Push it to Dockerhub

I REALLY NEED SOMEONE TO HELP ME OUT WITH THIS GENECLOUD OMICS WEBSITE. I REALLY NEED TO OPEN AND USE IT FOR MY MASTERS'S FINAL DISSERTATION AND THE DEADLINE IS VERY CLOSE!!! PLEASE HELP. IM NOT ABLE TO OPEN IT

Tested on R 4.2.0
All DT data tables cannot be displayed in release branch. The data tables in master branch still work.

Right now RAFSIL has only rafsil-1 / embedding plot, but we want to add two more plots

1. "rafsil-2 / embedding"
2. "correlation / embedding"

When I download to pdf, it generates html and inside the file says “An error has occurred”

For heatmap, what is the use for fold change or minimum column? If I change this, nothing changes

Error message on Sequence charge:

Listening on http://127.0.0.1:7565
[1] "P61981" "P62258" "P31947" "E9Q397" "Q9CQV8" "Q04917" "Q64514"
Internet connection problem occurs and the function will return the original error
Warning: Error in curl::curl_fetch_memory: Timeout was reached: [www.uniprot.org] Operation timed out after 4033 milliseconds with 0 out of 0 bytes received
182:

Right now, we have only heading text in the main panel of the microarray preprocessing section, but we want to add a loading icon & also few links about the sample data.

For PCA, the default is using all genes. The number I see for my data is 15077, when It should be 55000+. What happened to the remaining genes? Are they removed due to server/storage issues? If yes, we need to mention this

I tried scatter plot collage, it took forever and stopped

we DO NOT need to submit right? So, can we remove the Submit button for this?

Correlation should have a plot with samples or time as we often use in our papers. Giving the heatmap for correlation plot is not useful as it is a repeat from heatmap anyway. Pls update this after the paper has been submitted or accepted.

PCA 3-D is unable to rotate.

Right now, the code is very cluttered and won't follow any proper formatting.
There are many features that can be split into other files and called inside app.R which will make the code more consistent and easy to understand.

So New File Structure can be
-app.R
-functions (New Folder)
|---functionName.R

Linting tools like Styler can also be used.

Packages that could not be installed by scripts (or by remotes package) - tested on R 4.2.0

• RAFSIL (package not distributed)
• maEndToEnd (cannot install)
• cyjShiny(cannot install by scripts)
• RCyjs (have to use BiocManager)
• pd.hugene.1.0.st.v1 (have to use BiocManager)
  Other than that, RSQLite needs to be installed

Error: unused arguments (layoutName = "cola", styleFile = "./www/style/basicStyle.js")

read.csv automatically modify column names if the column names start with a number or special character. This name changing creates inconsistency between column names of input data file, and the meta data file
Error showed:

check if groups and column names are similar

if (!all(col_names %in% group_colnames) || ncol(groups) < 2) {
  showNotification(type = "error", "group names and DS column names not similar")
  return(NULL)
}