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).

Billing et al., Circulation, 2023

Billing et al., Circulation, 2023

• URL (proteome): https://kidneyapp.shinyapps.io/SGLT2i_proteome/
• URL (phosphoproteome): https://kidneyapp.shinyapps.io/SGLT2i_phosphoproteome/
• Maintainer: Vallon and Rinschen labs (La Jolla/Aarhus)
• Version: iSEE {2.8.0}, iSEEu {1.8.0}

More: A set of proteomic and phosphoproteomic datasets containing measurements for 5 organs (kidney, liver, heart, skeletal muscle, white adipose tissue (WAT)) of 2 mouse strains. Accompanies the publication Metabolic Communication by SGLT2 Inhibition.

Rigby et al., bioRxiv, 2023

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

FGCZ Fancy Single Cell Explorer (Index page).

• 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

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

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

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.

Kwon et al., bioRxiv, 2023

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.

iSEE COVID Hub

iSEE COVID Hub (Monocytes).

• 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

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

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.

Myocyte data sets

Myocyte data sets (Index page).

• URL: https://shiny.mdc-berlin.de/MyoExplorer/
• Maintainer: Max Delbrück Center
• Version: iSEE {2.6.0}

Upload your own SummarizedExperiment

Upload your own SummarizedExperiment (Index page).

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}

Tran et al., Neuron, 2021

Tran et al., Neuron, 2021 (AMY region).

• 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

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

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

CD8 TILs from B16 melanoma tumors.

• URL: https://tilatlas.shinyapps.io/B16_CD8TIL_10X/
• Maintainer: Swiss Portal for Immune Cell Analysis
• Version: iSEE {1.2.4}

Demonstration iSEE apps (2018)

Demonstration iSEE apps (CyTOF data set).

• 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.