osu-bmbl/iris

A Shiny web server for interactive visualization and analysis of RNA-seq data

iris's Issues

Submit count data (CSV): Maximum upload size exceeded

Hello,

I have installed locally but when I select my count data file it gives the above error. There are ~70,000 features and 190 samples = 32 MB csv file. Maybe line 118 of irisServer.R should have a larger arbitrary max size? It works if I shorten my file to under the current limit.

shiny.maxRequestSize = 30 * 1024^2,

Automatic remove duplicated row names

If the user's upload data contains duplicated row names, the IRIS server shows 'disconnected from server'

Salmon integration with IRIS-EDA

Allow for Salmon data output to read and analyzed via IRIS-EDA:

• Allow for txImport() capabilities
• Add Salmon check options to data input section
• Relevant workflow for edgeR, DESeq2, and limma-voom

Weblink down

Dear authors,
is the weblink for the portal down or not anymore supported?
regards

Shiny erro upon app execution

Hi!

when running your app like this:

shiny::runGitHub("iris", "OSU-BMBL")

i get the following error after first clicks in the GUI:

Warnung: Error in h: Fehler bei der Auswertung des Argumentes 'X' bei der Methodenauswahl für Funktion 'lapply': Fehler bei der Auswertung des Argumentes 'x' bei der Methodenauswahl für Funktion 'nrow':
[No stack trace available]

my sessionInfo:

sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 21.04

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] Biobase_2.50.0 viridis_0.6.1 tidyr_1.1.3
[4] tidygraph_1.2.0 bit64_4.0.5 viridisLite_0.4.0
[7] splines_4.0.4 ggraph_2.0.5 shadowtext_0.0.9
[10] DO.db_2.9 BiocManager_1.30.16 rvcheck_0.1.8
[13] stats4_4.0.4 blob_1.2.2 ggrepel_0.9.1
[16] pillar_1.6.2 RSQLite_2.2.8 lattice_0.20-45
[19] glue_1.4.2 downloader_0.4 digest_0.6.28
[22] RColorBrewer_1.1-2 polyclip_1.10-0 qvalue_2.22.0
[25] colorspace_2.0-2 ggfun_0.0.4 cowplot_1.1.1
[28] Matrix_1.3-4 plyr_1.8.6 pkgconfig_2.0.3
[31] clusterProfiler_3.18.1 purrr_0.3.4 GO.db_3.12.1
[34] scales_1.1.1 tweenr_1.0.2 enrichplot_1.10.2
[37] BiocParallel_1.24.1 ggforce_0.3.3 tibble_3.1.4
[40] generics_0.1.0 farver_2.1.0 IRanges_2.24.1
[43] ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6
[46] BiocGenerics_0.36.1 magrittr_2.0.1 crayon_1.4.1
[49] memoise_2.0.0 DOSE_3.16.0 fansi_0.5.0
[52] MASS_7.3-54 tools_4.0.4 data.table_1.14.0
[55] lifecycle_1.0.0 stringr_1.4.0 S4Vectors_0.28.1
[58] munsell_0.5.0 AnnotationDbi_1.52.0 compiler_4.0.4
[61] rlang_0.4.11 grid_4.0.4 igraph_1.2.6
[64] gtable_0.3.0 DBI_1.1.1 reshape2_1.4.4
[67] graphlayouts_0.7.1 R6_2.5.1 gridExtra_2.3
[70] dplyr_1.0.7 fastmap_1.1.0 bit_4.0.4
[73] utf8_1.2.2 fastmatch_1.1-3 fgsea_1.16.0
[76] GOSemSim_2.16.1 stringi_1.7.4 parallel_4.0.4
[79] Rcpp_1.0.7 vctrs_0.3.8 tidyselect_1.1.1
[82] scatterpie_0.1.7

is there any way i can fix this? sadly i cannot use your tool this way.
thanks for any help,
daaaaande

Install shiny on Windows 7

When I first typed
shiny::runGitHub("iris", "btmonier") on Rstudio, I got the error in the console that I haven't install the 'httpuv', after I manually installed httpuv package, I got the following error:
> shiny::runGitHub("iris", "btmonier") Downloading https://github.com/btmonier/iris/archive/master.tar.gz Error in utils::download.file(url, method = method, ...) : cannot open URL 'https://github.com/btmonier/iris/archive/master.tar.gz'

When I load the iris from desktop:

library(shiny)
setwd("C:/Users/flyku/Desktop/iris")
runApp()

The error:

Loading required package: Hmisc
Error: package or namespace load failed for ‘Hmisc’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘checkmate’
Loading required package: geneplotter
Loading required package: annotate
Error: package or namespace load failed for ‘annotate’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘RCurl’
Failed with error:  ‘package ‘annotate’ could not be loaded’
Loading required package: DESeq2
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘RCurl’
Failed with error:  ‘package ‘GenomeInfoDb’ could not be loaded’

after I installed all the dependencies, the browser says:ERROR: An error has occurred. Check your logs or contact the app author for clarification.

Listening on http://127.0.0.1:6333
Warning: Error in sub: input string 1 is invalid UTF-8
  [No stack trace available]
Warning: Error in sub: input string 1 is invalid UTF-8
  [No stack trace available]

Thanks.