Apps
+This page lists known public deployments of iSEE apps.
+Links are ordered in reverse order of iSEE package version (i.e., those using the most recent version appear first).
+Rigby et al., bioRxiv, 2023
+-
+
- URL: https://rehwinkellab.shinyapps.io/ifnresource/ +
- Maintainer: Rehwinkel group +
- Version: iSEE {2.12.0}, iSEEindex {0.99.13}, iSEEde {0.99.0} +
More: This app accompanies the preprint “Single-cell analysis of signalling and transcriptional responses to type I interferons” https://www.biorxiv.org/content/10.1101/2023.07.03.547491v1.
+FGCZ Fancy Single Cell Explorer
+-
+
- URL: https://fgcz-shiny.uzh.ch/fgcz_iSEE/ +
- Maintainer: Functional Genomics Center Zurich (FGCZ) +
- Version: iSEE {2.12.0} +
More: This app is listed at https://fgcz-shiny.uzh.ch/connect/, among other interactive apps from the same developer.
+Moffitt et al., Science, 2018
+-
+
- URL: https://moffittlab.connect.hms.harvard.edu/iSEE_hypothalamus/ +
- Maintainer: Center for Computational Biomedicine (CCB) Harvard Medical School and Moffitt Lab +
- Version: iSEE {2.10.0} +
More: This app showcases data from the article “Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region” https://www.science.org/doi/10.1126/science.aau5324 and is listed at https://moffittlab.connect.hms.harvard.edu/merfish/merfish_homepage.html, among other interactive apps from the same developer.
+Petukhov et al., Nat Biotech, 2021
+-
+
- URL: https://moffittlab.connect.hms.harvard.edu/iSEE_ileum/ +
- Maintainer: Center for Computational Biomedicine (CCB) Harvard Medical School and Moffitt Lab +
- Version: iSEE {2.10.0} +
More: This app showcases data from the article “Cell segmentation in imaging-based spatial transcriptomics” https://www.nature.com/articles/s41587-021-01044-w and is listed at https://moffittlab.connect.hms.harvard.edu/merfish/merfish_homepage.html, among other interactive apps from the same developer.
+Kim et al, JNeurosci, 2023.
+-
+
- URL: https://hbcc-nimh.shinyapps.io/shinyApp_JNS2023/ +
- Maintainer: Human Brain Collection Core (HBCC) - NIMH +
- Version: iSEE {2.10.0} +
More: This app accompanies the “Cellular Diversity in Human Subgenual Anterior Cingulate and Dorsolateral Prefrontal Cortex by Single-Nucleus RNASequencing” https://doi.org/10.1523/jneurosci.0830-22.2023.
+iSEE COVID Hub
+-
+
- URL (B cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Bcells/ +
- URL (Monocytes): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Monocytes +
- URL (NK cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_NKcells/ +
- URL (T cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Tcells +
- Maintainer: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) +
- Version: iSEE {2.9.0} +
More: Those apps are listed at http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT/.
+Kalucka et al., Cell, 2020
+-
+
- URL: https://vonandrian.connect.hms.harvard.edu/iSEE_Kalucka20_scECAtlas/ +
- Maintainer: von Andrian Laboratory +
- Version: iSEE {2.8.0}, iSEEu {1.5.2} +
More: This app showcases data from the article “Single-cell transcriptome atlas of murine endothelial cells” https://doi.org/10.1016/j.cell.2020.01.015.
+Brulois et al., Nat Commun, 2020
+-
+
- URL: https://vonandrian.connect.hms.harvard.edu/iSEE_Brulois20_PLN/ +
- Maintainer: von Andrian Laboratory +
- Version: iSEE {2.8.0}, iSEEu {1.5.2} +
More: This app showcases data from the article “A molecular map of murine lymph node blood vascular endothelium at single cell resolution” https://doi.org/10.1038/s41467-020-17291-5.
+Upload your own SummarizedExperiment
+This app allows visitors to upload an RDS file that contains a SummarizedExperiment object and another optional RDS file that contains an initial configuration object.
+-
+
- URL: https://ccb-rstudio-connect.hms.harvard.edu/iSEE_enterprise/ +
- Maintainer: Center for Computational Biomedicine (CCB) Harvard Medical School +
- Version: iSEE {2.4.0} +
Kwon et al., biorXiv, 2023
+This app showcases spatially resolved transcriptomics of the inferior temporal cortex, as pseudobulks.
+-
+
- URL: https://libd.shinyapps.io/Visium_SPG_AD_pseudobulk_AD_pathology_wholegenome/ +
- Maintainer: The Lieber Institute for Brain Development +
- Version: iSEE {2.10.0} +
More: This app accompanies the preprint “Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex” https://doi.org/10.1101/2023.04.20.537710.
+Myocyte data sets
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+
- URL: https://shiny.mdc-berlin.de/MyoExplorer/ +
- Maintainer: Max Delbrück Center +
- Version: iSEE {2.6.0} +
Tran et al., Neuron, 2021
+-
+
- URL: https://libd.shinyapps.io/tran2020_Amyg/ +
- URL: https://libd.shinyapps.io/tran2021_NAc/ +
- URL: https://libd.shinyapps.io/tran2021_sACC/ +
- URL: https://libd.shinyapps.io/tran2021_DLPFC/ +
- URL: https://libd.shinyapps.io/tran2021_AMY/ +
- URL: https://libd.shinyapps.io/tran2021_HPC/ +
- Maintainer: The Lieber Institute for Brain Development +
- Version: iSEE {2.4.0} +
More: Those apps accompany the article “Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain” https://www.cell.com/neuron/fulltext/S0896-6273(21)00655-3.
+Cristinelli et al., Front. Virol., 2021
+The authors developed HI-TEAM (HIV-Infected cell Transcriptome and EpitrAnscriptoMe), a user-friendly querying platform based on the iSEE interactive interface [iSEE] to explore all data or any gene of interest. More information is available at http://sib-pc17.unil.ch/HIVmain.html.
+-
+
- URL: https://hi-team.unil.ch/# +
- Maintainer: Ciuffi Lab +
- Version: iSEE {2.1.10}, iSEEu {1.1.4} +
More: This app accompanies the article “Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain” https://www.frontiersin.org/articles/10.3389/fviro.2021.714475/full.
+Comparison of SARS-CoV-1 and SARS-CoV-2
+-
+
- URL: https://shiny.mdc-berlin.de/COV/ +
- Maintainer: Max Delbrück Center +
- Version: iSEE {1.6.1} +
CD8 TILs from B16 melanoma tumors
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+
- URL: https://tilatlas.shinyapps.io/B16_CD8TIL_10X/ +
- Maintainer: Swiss Portal for Immune Cell Analysis +
- Version: iSEE {1.2.4} +
Demonstration iSEE apps (2018)
+-
+
- URL (single-cell RNA-seq, mouse visual cortex): https://marionilab.cruk.cam.ac.uk/iSEE_allen +
- URL (RNA-seq, The Cancer Genome Atlas): https://marionilab.cruk.cam.ac.uk/iSEE_tcga +
- URL (single-cell RNA-seq, peripheral blood mononuclear cells): https://marionilab.cruk.cam.ac.uk/iSEE_pbmc4k +
- URL (mass cytometry, healthy and diseased human donors): https://marionilab.cruk.cam.ac.uk/iSEE_cytof +
- Maintainer: Marioni group +
- Version: iSEE {1.2.4} +
More: Those apps are listed at https://marionilab.cruk.cam.ac.uk/, among other interactive apps from the same developer.
+ + +