Navigate to https://viafoundry.umassmed.edu/launcher/fulab
To view the app locally, there are two options.
-
Launch the app on a container that is pre-loaded with all dependencies.
-
Download the app code from github and install all dependencies manually.
- To run the app using docker first you must download the data to your local machine.
mkdir <path_to_app_data>
cd <path_to_app_data>
wget https://umms.dolphinnext.com/fulab/fu-multiomics-explorer-main/data/data.tar.gz
tar -xvf data.tar.gz
rm data.tar.gz
- Pull the container to your local machine.
docker pull quay.io/viascientific/fu-multiomics-explorer:1.0.2
- Open a terminal and execute the following command. You must replace
<path_to_app_data>with the path to the directory that contains the data you downloaded.
docker run --platform linux/amd64 -p 8789:8789 -v <path_to_app_data>:/home/app_data/ -ti quay.io/viascientific/fu-multiomics-explorer:1.0.2
- From any browser, navigate to http://localhost:8789/. The app will take about 30 seconds to fully load.
The explorer requires only a standard computer with enough RAM to support the in-memory operations.
The explorer is supported for macOS and Linux. The package has been tested on the following systems:
- macOS: Sequoia (15.5)
- Linux: Ubuntu (20.04.3 LTS)
shiny
Seurat
cyjShiny
jsonlite
dplyr
tidyr
ggplot2
readr
tibble
DT
shinycssloaders
svglite
shinyjs
bslib
bsicons
This code will clone the application from github and then download the input files. This will take about 2 minutes + the time it takes to download the input files (~3.2 Gb).
git clone https://github.com/ViaScientific/fu-multiomics-explorer.git
cd fu-multiomics-explorer/fu-multiomics-explorer/data
wget https://umms.dolphinnext.com/fulab/fu-multiomics-explorer-main/data/data.tar.gz
tar -xvf data.tar.gz
rm data.tar.gz
- Open a terminal and execute the following command. You must replace
<path_to_clone_location>with the path to the directory that contains the fu-multiomics-explorer directory that was downloaded from github.
R -e "shiny::runApp('<path_to_clone_location>/fu-multiomics-explorer/fu-multiomics-explorer/app.R')"
- From any browser, navigate to http://localhost:8789/. The app will take about 30 seconds to fully load.
The following files can be replaced with your own data (names must be exact). Not all files are required to run each section.
data/clean/metabolomic_metadata.txt
data/clean/B1.txt
data/clean/full_network.cyjs
data/clean/proteomic_metadata.txt
data/processed/A1_processed.txt
data/clean/sc-rnaseq_features.rds
data/raw/seurat_integrated.rds
data/raw/DEG/organic/*_2vs11_organic.csv
data/clean/transcriptomic_metadata.txt
data/raw/RNA_Count_by_donor_and_samples_beta_cells.csv
App-based analysis in the paper was performed in the following docker container: viascientific/multiomics-explorer-docker:1.0
The following is the corresponding sessionInfo() while performing any analysis included in the paper:
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinydashboard_0.7.2 shinycssloaders_1.0.0 DT_0.28
[4] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[7] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[10] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[13] tidyverse_2.0.0 igraph_1.4.3 cyjShiny_1.0.42
[16] base64enc_0.1-3 graph_1.78.0 BiocGenerics_0.46.0
[19] jsonlite_1.8.4 htmlwidgets_1.6.2 SeuratObject_4.1.3
[22] Seurat_4.3.0 shinyBS_0.61.1 shiny_1.7.4
loaded via a namespace (and not attached):
[1] deldir_1.0-9 pbapply_1.7-0 gridExtra_2.3
[4] rlang_1.1.1 magrittr_2.0.3 RcppAnnoy_0.0.20
[7] matrixStats_0.63.0 ggridges_0.5.4 compiler_4.3.0
[10] spatstat.geom_3.2-1 png_0.1-8 vctrs_0.6.2
[13] reshape2_1.4.4 pkgconfig_2.0.3 fastmap_1.1.1
[16] ellipsis_0.3.2 utf8_1.2.3 promises_1.2.0.1
[19] tzdb_0.4.0 goftest_1.2-3 later_1.3.1
[22] spatstat.utils_3.0-3 irlba_2.3.5.1 parallel_4.3.0
[25] cluster_2.1.4 R6_2.5.1 ica_1.0-3
[28] stringi_1.7.12 RColorBrewer_1.1-3 spatstat.data_3.0-1
[31] reticulate_1.28 parallelly_1.35.0 lmtest_0.9-40
[34] scattermore_1.1 Rcpp_1.0.10 tensor_1.5
[37] future.apply_1.11.0 zoo_1.8-12 sctransform_0.3.5
[40] timechange_0.2.0 httpuv_1.6.11 Matrix_1.5-1
[43] splines_4.3.0 tidyselect_1.2.0 abind_1.4-5
[46] spatstat.random_3.1-5 codetools_0.2-19 miniUI_0.1.1.1
[49] spatstat.explore_3.2-1 listenv_0.9.0 lattice_0.21-8
[52] plyr_1.8.8 withr_2.5.0 ROCR_1.0-11
[55] Rtsne_0.16 future_1.32.0 survival_3.5-5
[58] polyclip_1.10-4 fitdistrplus_1.1-11 pillar_1.9.0
[61] KernSmooth_2.23-20 stats4_4.3.0 plotly_4.10.1
[64] generics_0.1.3 sp_1.6-0 hms_1.1.3
[67] munsell_0.5.0 scales_1.2.1 globals_0.16.2
[70] xtable_1.8-4 glue_1.6.2 lazyeval_0.2.2
[73] tools_4.3.0 data.table_1.14.8 RANN_2.6.1
[76] leiden_0.4.3 cowplot_1.1.1 grid_4.3.0
[79] colorspace_2.1-0 nlme_3.1-162 patchwork_1.1.2
[82] cli_3.6.1 spatstat.sparse_3.0-1 fansi_1.0.4
[85] viridisLite_0.4.2 uwot_0.1.14 gtable_0.3.3
[88] digest_0.6.31 progressr_0.13.0 ggrepel_0.9.3
[91] htmltools_0.5.5 lifecycle_1.0.3 httr_1.4.6
[94] mime_0.12 MASS_7.3-59