This is a cool project, however it seems to me as if the images in the README.md file are not functional.

I tried three links, and all of them return

Invalid upstream response (403)

tomorrow, I run the debrowser as usual in R, but it stopped, the followed error seemed related to the shiny, I want to know how to solve this problem. please help me. debrowser is very important to me.

startDEBrowser()
Error in system(paste0("ls -t1 shiny_bookmarks", " | head -n 1"), intern = TRUE) :
'ls' not found

Hello nephantes,
I has been thinking about the normaliztion method in batch correction and normaliztion part in your platform analysis workflow. I only test your normaliztion part.And I find the MRN which is provided by DESeq2 and TMM method which is provided by edgeR from the source code of getNormalizeMatrix.I just want to ask you about the extent of the normalization of two methods.Because we know that the two methods is similar, they calculate respective scale factor at first.And then they should divided by scale factor, and DESeq2 prodvide counts(dds, normalized=T) to do this, and your MRN method also use this function do the normaliztion, and output result as normalized count matrix.
But edgeR do not provided the similar function. The cpm(dds, normalized.lib.sizes = TRUE) fucntion divided by the product of library-size and norm.factor(which it called effective size).So it go further a step than counts() function. But the DESeq2 provided vst/rlog fucntion to normalize the library size and also do the log2 transformation. Seem like the DESeq2 has go further a step than edgeR. then It seeming like we can't find similar function that do the same extent of normalization.So I think that is why you didn't use cpm() to do normalization. I find in TMM method ,you use equalizeLibSizes() function to do the normalization and output the pseudo.count matrix as the normalized count matrix. After see the source code of equalizeLibSizes(), I find it use the effective library size (which is same as mention in cpm()),but it didn't divided by the effective library size. and I think it is same like the counts() of DESeq2 in the extent of normalization in some way. I don't know if you agree with me.if so,I guess that' the reason you choose this method in edgeR. So my question is what do you think of the normaliztion part your provided in the platform. In other words, what do you think of the normalizetion of supplied by DESeq2 and edgeR?
My opinion is that the whole normalization included many steps. and every step is a part of normalization,will output normalized count matrix in every step. It will normalize some factor, such as like RNA compostion, GC-content, library-size,etc. And count divied by scale factor is to normalize the RNA compostion. but not librayr-size.That is the essence you provided in normalization part(although I was confused about waht does equalizeLibSizes() do)
And another quesion is the what count matrix you use to plot the pheatmap , boxplot and density plot. normalized matrix output from your normalzied part or log2 transformation or others? I'm doing the similar work , hope you can give me some suggestion Thanks in advance .Looking for your reply!

Hi,

I believe that the information you have provided at http://dolphin.readthedocs.org/en/master/debrowser/deseq.html#getting-started is insufficient to understand what the input TSV files should look like. I would add an explanation of what each column should contain and maybe explain in the vignette http://bioconductor.org/packages/devel/bioc/vignettes/debrowser/inst/doc/DEBrowser.html how to create those TSV files. Also, what are the units of the numbers? Counts? RPKM?

Also note that the information regarding these input files is incomplete on the vignette.

Best,
Leo

Hi
I am using the DEbrowser to do DE analysis, but it always report error when doing the DE analysis step in R 4.0.

Warning: Error in dots_list: lazy-load database '/usr/local/lib/R/4.0/site-library/debrowser/R/debrowser.rdb' is corrupt

Could you help to fix this bug?

Thanks.

Hi, I am painfully stuck at the first step..

Reporting error Colnames doesn't match with the metada table
Here is the link of my count matrix and metainfo, could you help me to check on it?

https://drive.google.com/file/d/1fZHLYVnGXeTmzbdgfwoZmJwb5pXr8qlf/view?usp=sharing
https://drive.google.com/file/d/1gofycjYEC5ctwhnJLqriwyTZAwK3Upd-/view?usp=sharing

Thanks!

Hello,
Thank you for the great package! It's really nice to give non-computational people ability to analyse RNA-seq data.

Though, is there any way to save analysis for future repeating? Any hand-made GUI analysis suffers from lack of reproducibility, and it looks like in your case, this problem can be fixed. Ideally, would be nice to have possibility to export R code, producing result. Or, at least, to save analysis parameters somewhere...

This is an upload file error that causes debrowser to quit.
I started with a toy example and this worked well, but as soon as I move into a larger subset of the data I get the same error:
Warning: Error in writeImpl: Text to be written must be a length-one character vector

Its very strange and I made sure to modify the sample names and check the collumns and add "gene name" to the count file ect.

I recall last year when I was using the project, there was a site which hosted a functional version at https://debrowser.umassmed.edu/ . I was wondering it the site was changed, or taken down, since it seems to just redirect to the bioconductor page?

Hi,

Both the vignette http://bioconductor.org/packages/devel/bioc/vignettes/debrowser/inst/doc/DEBrowser.html and the documentation on installed debrowser is more complicated than it needs to be now that debrowser is available via Bioconductor. Simply:

source("https://bioconductor.org/biocLite.R")
biocLite("debrowser")

is all you need. Although you might want to keep the Fedora and other details you have at http://dolphin.readthedocs.org/en/master/debrowser/local.html for those users.

Best,
Leo

Great job on the app! Always the perpetual question - "Well what if we change the parameters?", and this solves that plus adds a ton of useful secondary analyses. Definitely planning on introducing this to the lab.

Few minor bugs I noticed when using the test data set (or maybe they were features?):

1. I noticed two plots in the "Main Plots" section, one with data, and one that was empty. Not sure what the empty one is there for, or if it is a bug?
   

2. When selecting genes (maybe should be click driven instead of hover?) when the gene count gets high, it covers the y axis label of the sample gene counts plot.
   

3. In QC plots, when looking at the IQR and Density Plot, I found that there were two plots. Not sure what the second one is, but at least in the density plot, it is different that the first.

4. There is a random white box underneath the density plot and IQR plot views in the QC tab. Not sure if it is something that was supposed to computed and rendered, and it didn't happen?

If I inspect the element, it shows this as the link it is pulling from, I'm guessing its a temp file or something:
data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAdMAAAFNCAMAAABsTHWsAAAAA1BMVEX///+nxBvIAAAACXBIWXMAAAdhAAAHYQGVw7i2AAAArUlEQVR4nO3BMQEAAADCoPVP7WkJoAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABuYOIAAciSo5EAAAAASUVORK5CYII=

5. When I use the sorting functionality on the table view of the DEseq2 results which show count, fold change, p-value, etc., all of the sorting seems to work except the p-value and adjusted p-value which do unexpected sorting. Also the "p-adj" column shows up one two lines in one row sometimes, maybe make the column width larger?

Again, great job with everything! The one tool to rule them all!

To solve the installation problem about d3heatmap. You can use the commands below;

if (!require("devtools")) install.packages("devtools")
devtools::install_github("rstudio/d3heatmap")

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("debrowser")

Hi,

I find the selector you used for the padj cutoff to be very hard to use. It's not easy to use the mouse and select 0.05 or some other cutoff you want. I would consider using shiny::numericInput(, min = 0, max = 1, step = 0.01) instead (or another step value).

For example, I just had a hard time trying to get to 0.05 and would either get below it, or above it. The closest I got was 0.051.

Also, I couldn't find information on what type of method you are using to adjust the P-values. If you are controlling the FDR, I suggest changing the name to be more explicit to the type of error you are controlling in debrowser.

Best,
Leo

Dear Alper,

Sorry for opening a new thread. I didn't want to interfere with any issues Aviv might discover in his ongoing debugging attempts.

1. I took off the "-" dashes but it did not do anything.
   As far as I can tell, the problem seems to have been that the sequential order of the sample IDs in the Metadata File was not in complete accordance with the order of appearance of the same IDs in the Count Data File. After I rearranged the order I was able to continue to filter the data.

2. I still can't get the entire file to upload. I can successfully upload a Count Data File that reaches row number 15,905 along with the Metadata file. But anything beyond those 15,905 rows gives back the same error message:

Warning: Error in as.data.frame.default: cannot coerce class ‘"try-error"’ to a data.frame
  77: stop
  76: as.data.frame.default
  73: observeEventHandler
   2: runApp
   1: startDEBrowser

Upon inspection, I found nothing remarkable about line 15906.

3. After successfully uploading my trimmed Count file and it's respective Metadata
   
   I filter the data, go to DE Analysis and add a new comparison according to the Metadata file.
   If I choose DESeq, I get the following error message:

Warning: Error in DESeqDataSet: counts matrix should be numeric, currently it has mode: logical

If I choose EdgeR:

Warning: Error in rep: invalid 'times' argument

Any advice?

Thanks again for all the help,
Tom

I am trying to do an GOenrichment for my RNA-Seq (Arabidopsis) and am having trouble with the application in DEBrowser.
In the online version, I get an error that I am missing package org.At.tair(). I then switched to R and tried to run the GOenrichment after installing org.At.tair() and am now getting the error message "Error in .testforvalidKeys: None of the keys entered are valid keys for "SYMBOL"."
The application worked previously online for another lab member whithout any troubles and I am not sure what is going wrong. I am unfortunately a complete beginner with RNA-Seq analysis and R.
Thanks for your help!

I was playing around with the test data set, exited the app, then started the app again through startDEBrowser(), but I got an error

Error in system(paste0("ls -t1 shiny_bookmarks", " |  head -n 1"), intern = TRUE) : 
  'ls' not found

I was able to overcome this by deleting the shiny_bookmarks folder in Documents, then starting the app. Not sure if this has anything to do with the app at all, or if it's just some shiny default.

Hi,
I have an issue with uploading the files while I am pretty sure that names are the same I got this error:
Colnames doesn't match with the metada table

Would you please help me with this?
Here is the link of metadata and Counts matrix

https://drive.google.com/file/d/10i-XkIExsNBhDQdv4SKQFAcqjVOC0yfs/view?usp=sharing

https://drive.google.com/file/d/1VtuBciu8xvLzH112jm7XcQyT4JxGIb0R/view?usp=sharing

I have two questions about the input data:

1. I am not clear what the transcript column means. I used featurecounts (from the rsubread package) to create my count table, where the row names are the gene names predicted from the metagenome and all other columns comprise the unnormalized counts. But I am not clear what the transcript column represent.

2. I found this paper for an example on batch effects: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880143/

Batch effects are sub-groups of measurements that have qualitatively different behaviour across conditions and are unrelated to the biological or scientific variables in a study. For example, batch effects may occur if a subset of experiments was run on Monday and another set on Tuesday, if two technicians were responsible for different subsets of the experiments or if two different lots of reagents, chips or instruments were used. These effects are not exclusive to high-throughput biology and genomics research1, and batch effects also affect low-dimensional molecular measurements, such as northern blots and quantitative PCR. Although batch effects are difficult or impossible to detect in low-dimensional assays, high-throughput technologies provide enough data to detect and even remove them. However, if not properly dealt with, these effects can have a particularly strong and pervasive impact. Specific examples have been documented in published studies2,3 in which the biological variables were extremely correlated with technical variables, which subsequently led to serious concerns about the validity of the biological conclusions4,5.

Would this mean, that the batch column would have the value "1" for all samples if all were sampled from the same person/same day/same procedure?

Thank you very much!

Hi,

thanks for this great package!

For me, everything works fine except the downloading (snapshotting) of graphs.
It always gives me the same error (see title).

I tried it with two MACs and one windows pc - it's the same for all of them.

I updated all packages and run debrowser_1.11.9 on R 3.5.2

Is this a common error or did I just miss something you have to do/install prior to downloading all graphs?

Thanks for the help :).

Best regards,
Peter

Hi,

When you run debrowser locally and jump to the GO term tab without selecting genes, you don't get an error message or any indication that you should have selected some genes under the Main plots tab. Similarly for the Selected tab.

By the way, there's a tiny typo on the Main plots tab. It reads "For mor information;" instead of "For more information;".

Cheers,
Leo

Hi, thanks for the DEBrowser app, it is wonderful. I see I can download tables for up and down differentiated genes: can I download a table of only non-significant genes? Thank you,

Hugo

Hi,

Trying http://debrowser.umassmed.edu/ I ran frequently into "Disconnected from server" error messages. Sometimes even while running DESeq2 with the demo data.

You might want to consider giving users a longer connection timeout among other settings at http://www.shinyapps.io/ if that's what you are using.

Best,
Leo

As soon as I click submit for enrichgo or enrichkegg my shiny app crashes but does not disconnect console.

Hi,

Lets say that I want to select all the DE genes based on an adjusted p-value cutoff of 0.05 and a fold change of 3. The sliders on the left will then help me mark under the Main plots tab the genes that match this criteria. But how can I easily select these genes to then go to the GO term tab? Right now I find it a tad painful to have to click on all these genes on the Main plots tab. I might also miss-click and select a gene that does not match my criteria but is pretty close to one that I'm interested on. I have this problem regardless of whether I'm using the scatter, volcano plot or MAplot option at the Main plots tab.

Best,
Leo

Hello,
I encountered the above error while running DESeq. I know it's because I manually made the row.names of my matrix the name of the genes, but the example file ran with zero problems (https://informatics.fas.harvard.edu/differential-expression-with-deseq2.html). I checked that this file also has the gene names, instead of numericals, as the row names. I don't understand why they won't have the error message while I do.

This is what head(theirData) looks like: (dim = 6)

        dmel_unf1 dmel_unf2 dmel_unf3 dmel_inf1 dmel_inf2 dmel_inf3

FBgn0000003 209 164 143 162 80 151
FBgn0000008 572 467 580 509 435 297
FBgn0000014 387 276 383 289 237 141
FBgn0000015 158 123 157 117 110 70
FBgn0000017 2351 2126 2885 2896 2041 1467
FBgn0000018 368 296 314 318 272 169

This is what head(myData) looks like: (dim = 4)

CHIP_DHT1 CHIP_DHT2 CHIP_VEH1 CHIP_VEH2
A1BG 16 10 23 17
A1BG-AS1 26 15 20 22
A1CF 62 61 83 56
A2M 46 33 46 46
A2M-AS1 16 19 18 16
A2ML1 51 50 56 61

Any help is appreciated. Thanks!

Hi,

I think that it would be useful to display some reproducibility information. For example via devtools::session_info(). With this information a user can track which versions of the packages were used. For example, right now the deployed website at http://debrowser.umassmed.edu/ differs from the local version using debrowser version 0.99.0. At least one clear (although tiny) difference is the name of the tabs.

Best,
Leo

> options(width = 120)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------------
 setting  value                                    
 version  R version 3.3.0 alpha (2016-03-23 r70368)
 system   x86_64, darwin13.4.0                     
 ui       AQUA                                     
 language (EN)                                     
 collate  en_US.UTF-8                              
 tz       America/New_York                         
 date     2016-03-30                               

Packages ---------------------------------------------------------------------------------------------------------------
 package              * version  date       source        
 acepack                1.3-3.3  2014-11-24 CRAN (R 3.3.0)
 annotate               1.49.1   2016-02-06 Bioconductor  
 AnnotationDbi        * 1.33.7   2016-01-29 Bioconductor  
 assertthat             0.1      2013-12-06 CRAN (R 3.3.0)
 Biobase              * 2.31.3   2016-01-14 Bioconductor  
 BiocGenerics         * 0.17.3   2016-01-29 Bioconductor  
 BiocInstaller        * 1.21.4   2016-03-23 Bioconductor  
 BiocParallel           1.5.21   2016-03-23 Bioconductor  
 bitops                 1.0-6    2013-08-17 CRAN (R 3.3.0)
 caTools                1.17.1   2014-09-10 CRAN (R 3.3.0)
 cluster                2.0.3    2015-07-21 CRAN (R 3.3.0)
 clusterProfiler        2.5.6    2016-03-23 Bioconductor  
 colorspace             1.2-6    2015-03-11 CRAN (R 3.3.0)
 DBI                  * 0.3.1    2014-09-24 CRAN (R 3.3.0)
 debrowser            * 0.99.0   2016-03-25 Bioconductor  
 DESeq2                 1.11.32  2016-03-27 Bioconductor  
 devtools               1.10.0   2016-01-23 CRAN (R 3.3.0)
 digest                 0.6.9    2016-01-08 CRAN (R 3.3.0)
 DO.db                  2.9      2016-03-30 Bioconductor  
 DOSE                   2.9.6    2016-02-18 Bioconductor  
 dplyr                  0.4.3    2015-09-01 CRAN (R 3.3.0)
 DT                     0.1      2015-06-09 CRAN (R 3.3.0)
 edgeR                  3.13.5   2016-03-16 Bioconductor  
 foreign                0.8-66   2015-08-19 CRAN (R 3.3.0)
 Formula                1.2-1    2015-04-07 CRAN (R 3.3.0)
 gdata                  2.17.0   2015-07-04 CRAN (R 3.3.0)
 genefilter             1.53.3   2016-03-23 Bioconductor  
 geneplotter            1.49.0   2016-01-14 Bioconductor  
 GenomeInfoDb           1.7.6    2016-01-29 Bioconductor  
 GenomicRanges          1.23.24  2016-03-09 Bioconductor  
 ggplot2                2.1.0    2016-03-01 CRAN (R 3.3.0)
 ggvis                * 0.4.2    2015-06-06 CRAN (R 3.3.0)
 GO.db                  3.2.2    2016-03-24 Bioconductor  
 GOSemSim               1.29.2   2016-03-23 Bioconductor  
 gplots                 3.0.0    2016-03-28 CRAN (R 3.3.0)
 graph                  1.49.1   2016-01-14 Bioconductor  
 graphite               1.17.1   2016-02-02 Bioconductor  
 gridExtra              2.2.1    2016-02-29 CRAN (R 3.3.0)
 GSEABase               1.33.0   2016-01-14 Bioconductor  
 gtable                 0.2.0    2016-02-26 CRAN (R 3.3.0)
 gtools                 3.5.0    2015-05-29 CRAN (R 3.3.0)
 Hmisc                  3.17-2   2016-02-21 CRAN (R 3.3.0)
 htmltools              0.3.5    2016-03-21 CRAN (R 3.3.0)
 htmlwidgets            0.6      2016-02-25 CRAN (R 3.3.0)
 httpuv                 1.3.3    2015-08-04 CRAN (R 3.3.0)
 igraph                 1.0.1    2015-06-26 CRAN (R 3.3.0)
 IRanges              * 2.5.40   2016-03-11 Bioconductor  
 jsonlite               0.9.19   2015-11-28 CRAN (R 3.3.0)
 KernSmooth             2.23-15  2015-06-29 CRAN (R 3.3.0)
 lattice                0.20-33  2015-07-14 CRAN (R 3.3.0)
 latticeExtra           0.6-28   2016-02-09 CRAN (R 3.3.0)
 lazyeval               0.1.10   2015-01-02 CRAN (R 3.3.0)
 limma                  3.27.14  2016-03-23 Bioconductor  
 locfit                 1.5-9.1  2013-04-20 CRAN (R 3.3.0)
 magrittr               1.5      2014-11-22 CRAN (R 3.3.0)
 matrixStats            0.50.1   2015-12-15 CRAN (R 3.3.0)
 memoise                1.0.0    2016-01-29 CRAN (R 3.3.0)
 mime                   0.4      2015-09-03 CRAN (R 3.3.0)
 munsell                0.4.3    2016-02-13 CRAN (R 3.3.0)
 nnet                   7.3-12   2016-02-02 CRAN (R 3.3.0)
 org.Hs.eg.db         * 3.2.3    2016-03-24 Bioconductor  
 plyr                   1.8.3    2015-06-12 CRAN (R 3.3.0)
 qvalue                 2.3.2    2016-01-14 Bioconductor  
 R6                     2.1.2    2016-01-26 CRAN (R 3.3.0)
 rappdirs               0.3.1    2016-03-28 CRAN (R 3.3.0)
 RColorBrewer           1.1-2    2014-12-07 CRAN (R 3.3.0)
 Rcpp                   0.12.4   2016-03-26 CRAN (R 3.3.0)
 reactome.db            1.54.1   2016-03-30 Bioconductor  
 ReactomePA             1.15.5   2016-02-18 Bioconductor  
 reshape2               1.4.1    2014-12-06 CRAN (R 3.3.0)
 rpart                  4.1-10   2015-06-29 CRAN (R 3.3.0)
 RSQLite              * 1.0.0    2014-10-25 CRAN (R 3.3.0)
 S4Vectors            * 0.9.44   2016-03-28 Bioconductor  
 scales                 0.4.0    2016-02-26 CRAN (R 3.3.0)
 shiny                * 0.13.2   2016-03-28 CRAN (R 3.3.0)
 SparseM                1.7      2015-08-15 CRAN (R 3.3.0)
 stringi                1.0-1    2015-10-22 CRAN (R 3.3.0)
 stringr                1.0.0    2015-04-30 CRAN (R 3.3.0)
 SummarizedExperiment   1.1.22   2016-03-10 Bioconductor  
 survival               2.38-3   2015-07-02 CRAN (R 3.3.0)
 tidyr                  0.4.1    2016-02-05 CRAN (R 3.3.0)
 topGO                  2.23.3   2016-02-06 Bioconductor  
 XML                    3.98-1.4 2016-03-01 CRAN (R 3.3.0)
 xtable                 1.8-2    2016-02-05 CRAN (R 3.3.0)
 XVector                0.11.7   2016-02-13 Bioconductor  
 yaml                   2.1.13   2014-06-12 CRAN (R 3.3.0)
 zlibbioc               1.17.1   2016-03-19 Bioconductor 

Your DEBrowser is great. However, I get the error: "_scales_doColorRamp" not available for .Call() for package "scales" whenever i try to run an enrichGO or enrichKEGG analysis and click on the GO Term>Plot tab.

That‘s a good project! And I refer to a lot of your R source code.And there is a question.I didn't find the code describe of getNormalizedMatrix() in details.Could you show me which file it is in ?

FYI, while running reverse package dependency checks on R.rsp, your debrowser package came up with the below error (when running R CMD check --as-cran with _R_CHECK_LENGTH_1_CONDITION_=true).

*   checking examples ... ERROR
    ```
    Running examples in ‘debrowser-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: runHeatmap
    > ### Title: runHeatmap
    > ### Aliases: runHeatmap
    > 
    > ### ** Examples
    > 
    >     x <- runHeatmap(mtcars)
    Error in if (distance_method != "cor") { : the condition has length > 1
    Calls: runHeatmap -> heatmap.2 -> distfun
    Execution halted

Reproducibility / background

Set _R_CHECK_LENGTH_1_CONDITION_=true, which will be the default in next version of R, to get the error.
FYI, with _R_CHECK_LENGTH_1_CONDITION_=true we get:

> Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "true")
> if (1:2 == 1) TRUE
Error in if (1:2 == 1) TRUE : the condition has length > 1

whereas without we only get a warning:

> Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "false")

> if (1:2 == 1) TRUE
[1] TRUE
Warning message:
In if (1:2 == 1) TRUE :
  the condition has length > 1 and only the first element will be used

Hi,

I just looked at debrowser and I think that it's a great idea. It could be specially useful for teaching how to do RNA-seq data analysis without teaching R commands or for researchers that want to explore their DE results.

I found a list of technical issues or things I believe could be improved, see:

• Deployed website disconnects very frequently #11
• More reproducibility info? Deployed and local versions don't match #12
• Simplify installation instructions #13
• Explain in more detail the input TSV files #14
• GO term and Selected tabs needs a bit more explanation #15
• Improve selector for adjusted p-values cutoff
  #16
• How to select all DE genes? #17

I submitted them as independent issues so it'll be easier for you to track/address them.

Also note that you use DESeq in several parts of the app and the documentation when you really mean DESeq2. These are different packages so I would just encourage you to be crystal clear.

Thinking on the long run, you might want to explore using https://github.com/aoles/DEFormats (cc'ing @aoles) if you want to support multiple differential expression packages.

Overall, this is great work and I know that you just submitted your package to Bioc. I hope to see debrowser at Bioconductor for a long time.

Best,
Leo

Leonardo Collado Torres, PhD Candidate
Department of Biostatistics
Johns Hopkins University
Bloomberg School of Public Health
Website: http://lcolladotor.github.io/about.html

Hi, the DEBrowser is very useful. howeve,I found that I could not choose some other species, such as cattle, pigs and chickens, when I was doing GO enrichment analysis ? How to resolve this?

Hi, I'm able to load debrowser, and I'm able to start the shiny app by using startDEBrowser(), but I can't get the "Load Demo!", simple_demo.tsv, or advanced_demo.tsv to work. Nothing happens when I press the "Go to Analysis" button. I haven't worked much with Shiny apps, so I don't know how to troubleshoot the process, but since it's a web app, my first instinct was to go to the web console. I found that every time I hit the submit button, it would give me 6 new errors, and they are all the same, and roughly repetitive. I've attached the error messages I got in the console, although I don't know if it will help.

I've also tried running it on 64x Windows 8.1 and macOS Sierra 10.12.6, and it seems to do the same thing.

Hello,
I have selected a tab-delimited count table and a tab-delimited metadata file for upload to your web instance of DEBrowser. The status bar below each selected files states 'upload complete' for both files, but there is no upload summary. If I press the 'Upload' button then I receive an error message stating that I was diconnedted from server and I have to 'Reload'
See attached screenshots:

Any suggestion how to proceed?

When trying to upload a large (~100 MB) count data file, shiny reports that the maximum upload size is exceeded.

Hello,

I was trying to run DE analysis with DESeq2 from DEBrowser (v1.21.1), but it keeps generating errors as shown below whenever I select any type of shrinkage methods (apeglm, ashr, or normal) with Wald test:

Warning: Error in h: error in evaluating the argument 'x' in selecting a method for function 'nrow': subscript contains invalid names
2: runApp
1: startDEBrowser
Warning: Error in h: error in evaluating the argument 'x' in selecting a method for function 'nrow': subscript contains invalid names
49:

Could you please explain why this is happening?

Thanks!

It seems this is related to the recent upgrade of the shiny package to version 1.0.4. You can install version 1.0.3 using the command below. Restart R studio and run this command before loading the library.

install_version("shiny", version = "1.0.3", repos = "http://cran.us.r-project.org")

And load and start DEBrowser

  library(debrowser) 
  startDEBrowser()

Hi

Great browser!!! I am having trouble when i try to select a category on my meta file such as treatment or condition or time from the browser to re-draw the PCA. I get the following error

Error in : Must request at least one colour from a hue palette

This does not happen with demo data?

few lines from my metafile are attached:

example_meta.xlsx

Have you seen this before?

> library(devtools)
> install_github('UMMS-Biocore/debrowser')
Downloading GitHub repo UMMS-Biocore/debrowser@master
from URL https://api.github.com/repos/UMMS-Biocore/debrowser/zipball/master
Installing debrowser
Installation failed: row names contain missing values

I'm trying to load a tsv to DEBrowser, which does not contain transcript IDs. They have been removed by our internal pipeline. So I just have genes and counts. And of course a metadata file.

I even tried creating a fake transcript column but am getting the same error. All the demos work fine for me.

I'm sure I could figure this out on my own but the error report is pretty vague.

Hi everybody please I need your help

I am a beginner in bioinformatics and R, so my issue is that I have a dataset as you see in my screenshot with 26 genes and 1083 samples ( from TCGA) I want to do the RNA seq analysis in two conditions, I tried different script but I failed, please can someone help me?

Hello there.

Recently I discovered this usefull program but whenever I try to upload my Count Data and Metadata, always this occurs:

Listening on http://127.0.0.1:4733
Warning: Error in as.data.frame.default: cannot coerce class ‘"try-error"’ to a data.frame
2: runApp
1: startDEBrowser

I'm not good at with bioinformatic tools, so is there any problem with my installing or data?
Could you help me for this instance, please?

Best regards.

This is great. Thanks.

Is there any way to launch debrowser from shiny server?

I installed debrowser with biocLite() from Rstudio server on the same host that is running my shiny server, and it works from there (or at least gets to the data load page)

From my home dir, I did

git clone https://github.com/UMMS-Biocore/debrowser.git
cd /srv/shiny-server/
sudo ln -s ~/debrowser/R debrowser
sudo chmod -R 777 debrowser

Visiting http://server:3838/debrowser/ gets me the Escher-like splash screen, along with the message

Disconnected from the server.

I also tried putting the following in an app.R (knowing that it was a long-shot):

library(debrowser)
startDEBrowser()

which gave

An error has occurred

The application failed to start.

The application exited during initialization.

Do you already have this in your documentation? Or is there a place for users to contribute tips?

For the GitHub version of DEBrowser (as of 2018-08-23 08:30 EDT) running in Ubuntu 18.04 LTS, the following system libraries are required.

Actually, I'm not sure which of the udunits components is required.

sudo apt-get install libcurl4-openssl-dev libssl-dev libv8-3.14-dev \
    udunits-bin libudunits2-* libxml2-dev 

Which R version is compatible with debrowser? I am getting the error mentioned in the title when I try to install it with biocLite.

Hi, when I try to access (https://bioinfo.umassmed.edu/pub/debrowser/advanced_demo.tsv) and (https://bioinfo.umassmed.edu/pub/debrowser/simple_demo.tsv), I get a not found error.

I just installed DEBrowser 1df2b83 and it looks great. Thanks.

In the past (#159), I was told that a lot of manual intervention was required to get DEBrowser running under Shiny Server. Is that still the case? Have the requirements changed in any way?

BTW I didn't get the latest version from Bioconductor like the readme suggests

source(“https://www.bioconductor.org/biocLite.R”)
biocLite("debrowser")

I "had" to get it from GitHub with devtools

install.packages("devtools")
library(devtools)
install_github('UMMS-Biocore/debrowser')

Otherwise I still got the older version where TSV imports were required and the file selection boxes were stacked vertically.

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)