From f976317ebd708dade2d4b5961cb6e90eeee4fc82 Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Wed, 22 Nov 2023 07:45:48 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- about.html | 29 ++- apps.html | 583 +++++++++++++++++++++++++++++++++++++++++++++++++ dashboard.html | 27 ++- gallery.html | 29 ++- index.html | 27 ++- panels.html | 27 ++- resources.html | 27 ++- search.json | 104 ++++----- sitemap.xml | 14 +- 10 files changed, 747 insertions(+), 122 deletions(-) create mode 100644 apps.html diff --git a/.nojekyll b/.nojekyll index fc8c20b..bdf14bd 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -e15c8172 \ No newline at end of file +739bb06d \ No newline at end of file diff --git a/about.html b/about.html index ccb3c79..b97fa5f 100644 --- a/about.html +++ b/about.html @@ -84,22 +84,29 @@
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    Contributors
    diff --git a/apps.html b/apps.html new file mode 100644 index 0000000..a45437f --- /dev/null +++ b/apps.html @@ -0,0 +1,583 @@ + + + + + + + + + +iSEE - Apps + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Apps

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    This page lists known public deployments of iSEE apps.

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    Links are ordered in reverse order of iSEE package version (i.e., those using the most recent version appear first).

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    Rigby et al., bioRxiv, 2023

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    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.

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    FGCZ Fancy Single Cell Explorer

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    More: This app is listed at https://fgcz-shiny.uzh.ch/connect/, among other interactive apps from the same developer.

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    Moffitt et al., Science, 2018

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    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.

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    Petukhov et al., Nat Biotech, 2021

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    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.

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    Kim et al, JNeurosci, 2023.

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    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.

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    iSEE COVID Hub

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    More: Those apps are listed at http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT/.

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    Kalucka et al., Cell, 2020

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    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.

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    Brulois et al., Nat Commun, 2020

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    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.

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    Upload your own SummarizedExperiment

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    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.

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    Kwon et al., biorXiv, 2023

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    This app showcases spatially resolved transcriptomics of the inferior temporal cortex, as pseudobulks.

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    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.

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    Myocyte data sets

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    Tran et al., Neuron, 2021

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    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.

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    Cristinelli et al., Front. Virol., 2021

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    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.

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    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.

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    Comparison of SARS-CoV-1 and SARS-CoV-2

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    CD8 TILs from B16 melanoma tumors

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    Demonstration iSEE apps (2018)

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    More: Those apps are listed at https://marionilab.cruk.cam.ac.uk/, among other interactive apps from the same developer.

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  • Home -
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    Demonstration } } var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); - var filterRegex = new RegExp("https:\/\/iSEE\.github\.io\/"); + var filterRegex = new RegExp('/' + window.location.host + '/'); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href); } diff --git a/index.html b/index.html index 639a0b0..8f6c837 100644 --- a/index.html +++ b/index.html @@ -84,22 +84,29 @@
  • Home -
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  • - Resources + Learn
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  • diff --git a/panels.html b/panels.html index c7ce2b2..22d2132 100644 --- a/panels.html +++ b/panels.html @@ -84,22 +84,29 @@
  • Home -
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  • diff --git a/resources.html b/resources.html index c053acd..2c83606 100644 --- a/resources.html +++ b/resources.html @@ -84,22 +84,29 @@
  • Home -
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  • diff --git a/search.json b/search.json index 0535f05..db6a532 100644 --- a/search.json +++ b/search.json @@ -49,121 +49,121 @@ "text": "Our YouTube channel includes videos documenting and demonstrating iSEE apps in action.\nhttps://www.youtube.com/@iSEEdevelopers" }, { - "objectID": "gallery.html", - "href": "gallery.html", - "title": "Gallery", + "objectID": "apps.html", + "href": "apps.html", + "title": "Apps", "section": "", "text": "This page lists known public deployments of iSEE apps.\nLinks are ordered in reverse order of iSEE package version (i.e., those using the most recent version appear first)." }, { - "objectID": "gallery.html#rigby-et-al.-biorxiv-2023", - "href": "gallery.html#rigby-et-al.-biorxiv-2023", - "title": "Gallery", + "objectID": "apps.html#rigby-et-al.-biorxiv-2023", + "href": "apps.html#rigby-et-al.-biorxiv-2023", + "title": "Apps", "section": "Rigby et al., bioRxiv, 2023", "text": "Rigby et al., bioRxiv, 2023\n\nURL: https://rehwinkellab.shinyapps.io/ifnresource/\nMaintainer: Rehwinkel group\nVersion: iSEE {2.12.0}, iSEEindex {0.99.13}, iSEEde {0.99.0}\n\nMore: 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." }, { - "objectID": "gallery.html#fgcz-fancy-single-cell-explorer", - "href": "gallery.html#fgcz-fancy-single-cell-explorer", - "title": "Gallery", + "objectID": "apps.html#fgcz-fancy-single-cell-explorer", + "href": "apps.html#fgcz-fancy-single-cell-explorer", + "title": "Apps", "section": "FGCZ Fancy Single Cell Explorer", "text": "FGCZ Fancy Single Cell Explorer\n\nURL: https://fgcz-shiny.uzh.ch/fgcz_iSEE/\nMaintainer: Functional Genomics Center Zurich (FGCZ)\nVersion: iSEE {2.12.0}\n\nMore: This app is listed at https://fgcz-shiny.uzh.ch/connect/, among other interactive apps from the same developer." }, { - "objectID": "gallery.html#moffitt-et-al.-science-2018", - "href": "gallery.html#moffitt-et-al.-science-2018", - "title": "Gallery", + "objectID": "apps.html#moffitt-et-al.-science-2018", + "href": "apps.html#moffitt-et-al.-science-2018", + "title": "Apps", "section": "Moffitt et al., Science, 2018", "text": "Moffitt et al., Science, 2018\n\nURL: https://moffittlab.connect.hms.harvard.edu/iSEE_hypothalamus/\nMaintainer: Center for Computational Biomedicine (CCB) Harvard Medical School and Moffitt Lab\nVersion: iSEE {2.10.0}\n\nMore: 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." }, { - "objectID": "gallery.html#petukhov-et-al.-nat-biotech-2021", - "href": "gallery.html#petukhov-et-al.-nat-biotech-2021", - "title": "Gallery", + "objectID": "apps.html#petukhov-et-al.-nat-biotech-2021", + "href": "apps.html#petukhov-et-al.-nat-biotech-2021", + "title": "Apps", "section": "Petukhov et al., Nat Biotech, 2021", "text": "Petukhov et al., Nat Biotech, 2021\n\nURL: https://moffittlab.connect.hms.harvard.edu/iSEE_ileum/\nMaintainer: Center for Computational Biomedicine (CCB) Harvard Medical School and Moffitt Lab\nVersion: iSEE {2.10.0}\n\nMore: 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." }, { - "objectID": "gallery.html#kim-et-al-jneurosci-2023.", - "href": "gallery.html#kim-et-al-jneurosci-2023.", - "title": "Gallery", + "objectID": "apps.html#kim-et-al-jneurosci-2023.", + "href": "apps.html#kim-et-al-jneurosci-2023.", + "title": "Apps", "section": "Kim et al, JNeurosci, 2023.", "text": "Kim et al, JNeurosci, 2023.\n\nURL: https://hbcc-nimh.shinyapps.io/shinyApp_JNS2023/\nMaintainer: Human Brain Collection Core (HBCC) - NIMH\nVersion: iSEE {2.10.0}\n\nMore: 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." }, { - "objectID": "gallery.html#isee-covid-hub", - "href": "gallery.html#isee-covid-hub", - "title": "Gallery", + "objectID": "apps.html#isee-covid-hub", + "href": "apps.html#isee-covid-hub", + "title": "Apps", "section": "iSEE COVID Hub", "text": "iSEE COVID Hub\n\nURL (B cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Bcells/\nURL (Monocytes): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Monocytes\nURL (NK cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_NKcells/\nURL (T cells): http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT_Tcells\nMaintainer: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)\nVersion: iSEE {2.9.0}\n\nMore: Those apps are listed at http://shiny.imbei.uni-mainz.de:3838/iSEE_covidIT/." }, { - "objectID": "gallery.html#kalucka-et-al.-cell-2020", - "href": "gallery.html#kalucka-et-al.-cell-2020", - "title": "Gallery", + "objectID": "apps.html#kalucka-et-al.-cell-2020", + "href": "apps.html#kalucka-et-al.-cell-2020", + "title": "Apps", "section": "Kalucka et al., Cell, 2020", "text": "Kalucka et al., Cell, 2020\n\nURL: https://vonandrian.connect.hms.harvard.edu/iSEE_Kalucka20_scECAtlas/\nMaintainer: von Andrian Laboratory\nVersion: iSEE {2.8.0}, iSEEu {1.5.2}\n\nMore: 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." }, { - "objectID": "gallery.html#brulois-et-al.-nat-commun-2020", - "href": "gallery.html#brulois-et-al.-nat-commun-2020", - "title": "Gallery", + "objectID": "apps.html#brulois-et-al.-nat-commun-2020", + "href": "apps.html#brulois-et-al.-nat-commun-2020", + "title": "Apps", "section": "Brulois et al., Nat Commun, 2020", "text": "Brulois et al., Nat Commun, 2020\n\nURL: https://vonandrian.connect.hms.harvard.edu/iSEE_Brulois20_PLN/\nMaintainer: von Andrian Laboratory\nVersion: iSEE {2.8.0}, iSEEu {1.5.2}\n\nMore: 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." }, { - "objectID": "gallery.html#upload-your-own-summarizedexperiment", - "href": "gallery.html#upload-your-own-summarizedexperiment", - "title": "Gallery", + "objectID": "apps.html#upload-your-own-summarizedexperiment", + "href": "apps.html#upload-your-own-summarizedexperiment", + "title": "Apps", "section": "Upload your own SummarizedExperiment", "text": "Upload your own SummarizedExperiment\nThis app allows visitors to upload an RDS file that contains a SummarizedExperiment object and another optional RDS file that contains an initial configuration object.\n\nURL: https://ccb-rstudio-connect.hms.harvard.edu/iSEE_enterprise/\nMaintainer: Center for Computational Biomedicine (CCB) Harvard Medical School\nVersion: iSEE {2.4.0}" }, { - "objectID": "gallery.html#kwon-et-al.-biorxiv-2023", - "href": "gallery.html#kwon-et-al.-biorxiv-2023", - "title": "Gallery", + "objectID": "apps.html#kwon-et-al.-biorxiv-2023", + "href": "apps.html#kwon-et-al.-biorxiv-2023", + "title": "Apps", "section": "Kwon et al., biorXiv, 2023", "text": "Kwon et al., biorXiv, 2023\nThis app showcases spatially resolved transcriptomics of the inferior temporal cortex, as pseudobulks.\n\nURL: https://libd.shinyapps.io/Visium_SPG_AD_pseudobulk_AD_pathology_wholegenome/\nMaintainer: The Lieber Institute for Brain Development\nVersion: iSEE {2.10.0}\n\nMore: 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." }, { - "objectID": "gallery.html#myocyte-data-sets", - "href": "gallery.html#myocyte-data-sets", - "title": "Gallery", + "objectID": "apps.html#myocyte-data-sets", + "href": "apps.html#myocyte-data-sets", + "title": "Apps", "section": "Myocyte data sets", "text": "Myocyte data sets\n\nURL: https://shiny.mdc-berlin.de/MyoExplorer/\nMaintainer: Max Delbrück Center\nVersion: iSEE {2.6.0}" }, { - "objectID": "gallery.html#tran-et-al.-neuron-2021", - "href": "gallery.html#tran-et-al.-neuron-2021", - "title": "Gallery", + "objectID": "apps.html#tran-et-al.-neuron-2021", + "href": "apps.html#tran-et-al.-neuron-2021", + "title": "Apps", "section": "Tran et al., Neuron, 2021", "text": "Tran et al., Neuron, 2021\n\nURL: https://libd.shinyapps.io/tran2020_Amyg/\nURL: https://libd.shinyapps.io/tran2021_NAc/\nURL: https://libd.shinyapps.io/tran2021_sACC/\nURL: https://libd.shinyapps.io/tran2021_DLPFC/\nURL: https://libd.shinyapps.io/tran2021_AMY/\nURL: https://libd.shinyapps.io/tran2021_HPC/\nMaintainer: The Lieber Institute for Brain Development\nVersion: iSEE {2.4.0}\n\nMore: 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." }, { - "objectID": "gallery.html#cristinelli-et-al.-front.-virol.-2021", - "href": "gallery.html#cristinelli-et-al.-front.-virol.-2021", - "title": "Gallery", + "objectID": "apps.html#cristinelli-et-al.-front.-virol.-2021", + "href": "apps.html#cristinelli-et-al.-front.-virol.-2021", + "title": "Apps", "section": "Cristinelli et al., Front. Virol., 2021", "text": "Cristinelli et al., Front. Virol., 2021\nThe 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.\n\nURL: https://hi-team.unil.ch/#\nMaintainer: Ciuffi Lab\nVersion: iSEE {2.1.10}, iSEEu {1.1.4}\n\nMore: 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." }, { - "objectID": "gallery.html#comparison-of-sars-cov-1-and-sars-cov-2", - "href": "gallery.html#comparison-of-sars-cov-1-and-sars-cov-2", - "title": "Gallery", + "objectID": "apps.html#comparison-of-sars-cov-1-and-sars-cov-2", + "href": "apps.html#comparison-of-sars-cov-1-and-sars-cov-2", + "title": "Apps", "section": "Comparison of SARS-CoV-1 and SARS-CoV-2", "text": "Comparison of SARS-CoV-1 and SARS-CoV-2\n\nURL: https://shiny.mdc-berlin.de/COV/\nMaintainer: Max Delbrück Center\nVersion: iSEE {1.6.1}" }, { - "objectID": "gallery.html#cd8-tils-from-b16-melanoma-tumors", - "href": "gallery.html#cd8-tils-from-b16-melanoma-tumors", - "title": "Gallery", + "objectID": "apps.html#cd8-tils-from-b16-melanoma-tumors", + "href": "apps.html#cd8-tils-from-b16-melanoma-tumors", + "title": "Apps", "section": "CD8 TILs from B16 melanoma tumors", "text": "CD8 TILs from B16 melanoma tumors\n\nURL: https://tilatlas.shinyapps.io/B16_CD8TIL_10X/\nMaintainer: Swiss Portal for Immune Cell Analysis\nVersion: iSEE {1.2.4}" }, { - "objectID": "gallery.html#demonstration-isee-apps-2018", - "href": "gallery.html#demonstration-isee-apps-2018", - "title": "Gallery", + "objectID": "apps.html#demonstration-isee-apps-2018", + "href": "apps.html#demonstration-isee-apps-2018", + "title": "Apps", "section": "Demonstration iSEE apps (2018)", "text": "Demonstration iSEE apps (2018)\n\nURL (single-cell RNA-seq, mouse visual cortex): https://marionilab.cruk.cam.ac.uk/iSEE_allen\nURL (RNA-seq, The Cancer Genome Atlas): https://marionilab.cruk.cam.ac.uk/iSEE_tcga\nURL (single-cell RNA-seq, peripheral blood mononuclear cells): https://marionilab.cruk.cam.ac.uk/iSEE_pbmc4k\nURL (mass cytometry, healthy and diseased human donors): https://marionilab.cruk.cam.ac.uk/iSEE_cytof\nMaintainer: Marioni group\nVersion: iSEE {1.2.4}\n\nMore: Those apps are listed at https://marionilab.cruk.cam.ac.uk/, among other interactive apps from the same developer." }, @@ -214,7 +214,7 @@ "href": "about.html#contributors", "title": "About", "section": "Contributors", - "text": "Contributors\nWe thank our community who contributed code, ideas, bug reports, and feature requests over the years!\nSpecial thanks to:\n\nLeonardo Collado-Torres for contributions to our GitHub Action workflow.\nMichael Stadler for contributing the reduced dimension mode in iSEEu\nThomas Sandmann for supporting the development of iSEEhub, iSEEindex, iSEEde, and iSEEpathways, as well as contributing to the vignette of iSEEde." + "text": "Contributors\nWe thank our community who contributed code, ideas, bug reports, and feature requests over the years!\nSpecial thanks to:\n\nLeonardo Collado-Torres for contributions to our GitHub Action workflow.\nMichael Stadler for contributing the reduced dimension mode in iSEEu\nThomas Sandmann for supporting the development of iSEEhub, iSEEindex, iSEEde, and iSEEpathways." }, { "objectID": "about.html#code-of-conduct", diff --git a/sitemap.xml b/sitemap.xml index fee8426..b3e2e50 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,26 +2,26 @@ https://iSEE.github.io/resources.html - 2023-11-21T21:16:28.479Z + 2023-11-22T07:45:48.476Z - https://iSEE.github.io/gallery.html - 2023-11-21T21:16:27.473Z + https://iSEE.github.io/apps.html + 2023-11-22T07:45:47.456Z https://iSEE.github.io/dashboard.html - 2023-11-21T21:16:26.369Z + 2023-11-22T07:45:46.307Z https://iSEE.github.io/panels.html - 2023-11-21T21:16:25.855Z + 2023-11-22T07:45:45.771Z https://iSEE.github.io/index.html - 2023-11-21T21:16:26.827Z + 2023-11-22T07:45:46.797Z https://iSEE.github.io/about.html - 2023-11-21T21:16:27.960Z + 2023-11-22T07:45:47.944Z