awesome-isee-apps

List of known iSEE apps publicly deployed

iSEE for proteome and phosphoproteome

• 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.

Collection of single-cell data sets using iSEEindex

• 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.

iSEEindex demo

• URL: https://isee.shinyapps.io/iSEEindex-demo/
• Maintainer: iSEE developers
• Version: iSEE {2.12.0}, iSEEindex {0.99.8}

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.

MERFISH mouse data sets

• URL (hypothalamus): https://moffittlab.connect.hms.harvard.edu/iSEE_hypothalamus/
• URL (ileum): 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: Those apps are listed at https://moffittlab.connect.hms.harvard.edu/merfish/merfish_homepage.html.

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/.

Upload your own SummarizedExperiment (CCB HMS)

• URL: https://ccb-rstudio-connect.hms.harvard.edu/iSEE_enterprise/
• Maintainer: Center for Computational Biomedicine (CCB) Harvard Medical School
• Version: iSEE {2.4.0}

Spatially resolved transcriptomics of the inferior temporal cortex (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 article https://doi.org/10.1101/2023.04.20.537710

Myocyte data sets

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

Single-nucleus transcriptome analysis in human brain

• 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 https://www.cell.com/neuron/fulltext/S0896-6273(21)00655-3

HI-TEAM (HIV-Infected cell Transcriptome and EpitrAnscriptoMe)

• URL: https://hi-team.unil.ch/#
• Maintainer: Ciuffi Lab
• Version: iSEE {2.1.10}, iSEEu {1.1.4}

More: This app accompanies the article 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

• 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.