osu-bmbl / iris Goto Github PK
View Code? Open in Web Editor NEWA Shiny web server for interactive visualization and analysis of RNA-seq data
Home Page: https://bmbls.bmi.osumc.edu/IRIS/
License: GNU General Public License v3.0
A Shiny web server for interactive visualization and analysis of RNA-seq data
Home Page: https://bmbls.bmi.osumc.edu/IRIS/
License: GNU General Public License v3.0
If the user's upload data contains duplicated row names, the IRIS server shows 'disconnected from server'
Allow for Salmon data output to read and analyzed via IRIS-EDA:
txImport()
capabilitiesDear authors,
is the weblink for the portal down or not anymore supported?
regards
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.
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,
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
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