diff --git a/inst/templates/SCFeatBarcoding.Rmd b/inst/templates/SCFeatBarcoding.Rmd index df3c14140..a2af1735e 100644 --- a/inst/templates/SCFeatBarcoding.Rmd +++ b/inst/templates/SCFeatBarcoding.Rmd @@ -481,7 +481,7 @@ AUCell_plotTSNE(tSNE=cellsTsne, The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"} ### Data availability diff --git a/inst/templates/SCLabelClusters.Rmd b/inst/templates/SCLabelClusters.Rmd index bbed03149..7a3f3e175 100755 --- a/inst/templates/SCLabelClusters.Rmd +++ b/inst/templates/SCLabelClusters.Rmd @@ -325,7 +325,7 @@ kable_styling("striped", full_width = F, position = "left") The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Celltype Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Celltype Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Celltype Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Celltype Report"),"/sce_h5")}`){target="_blank"} ### Data availability diff --git a/inst/templates/ScSCE.Rmd b/inst/templates/ScSCE.Rmd index 3ec7029ed..2874603f4 100644 --- a/inst/templates/ScSCE.Rmd +++ b/inst/templates/ScSCE.Rmd @@ -415,7 +415,7 @@ AUCell_plotTSNE(tSNE=cellsTsne, The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Cluster Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("SC Cluster Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`){target="_blank"} ### Data availability diff --git a/inst/templates/ScSCECombine.Rmd b/inst/templates/ScSCECombine.Rmd index 931645fa6..19a07d53b 100644 --- a/inst/templates/ScSCECombine.Rmd +++ b/inst/templates/ScSCECombine.Rmd @@ -300,7 +300,7 @@ p2 The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"} ### Methods diff --git a/inst/templates/ScSeurat.Rmd b/inst/templates/ScSeurat.Rmd index 0db846990..246746c67 100644 --- a/inst/templates/ScSeurat.Rmd +++ b/inst/templates/ScSeurat.Rmd @@ -472,7 +472,7 @@ AUCell_plotTSNE(tSNE=cellsUmap, The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", sample(0:9, size=1), "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {paste0("https://fgcz-shiny.uzh.ch/fgcz_iSEE", sample(0:9, size=1), "/?data=",output$getColumn("SC Cluster Report"),"/sce_h5")}`){target="_blank"} ### Data availability diff --git a/inst/templates/ScSeuratCombine.Rmd b/inst/templates/ScSeuratCombine.Rmd index 4fb35b01a..d5fe6ef6f 100644 --- a/inst/templates/ScSeuratCombine.Rmd +++ b/inst/templates/ScSeuratCombine.Rmd @@ -377,7 +377,7 @@ AUCell_plotTSNE(tSNE=cellsTsne, The iSEE (Interactive SummarizedExperiment Explorer) explorer provides a general visual interface for exploring single cell data. iSEE allows users to simultaneously visualize multiple aspects of a given data set, including experimental data, metadata, and analysis results. Dynamic linking and point selection facilitate the flexible exploration of interactions between different data aspects. [Rue-Albrecht K, Marini F, Soneson C, Lun ATL (2018). “iSEE: Interactive SummarizedExperiment Explorer.” F1000Research, 7, 741. doi: 10.12688/f1000research.14966.1.] -The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`) +The iSEE shiny app can be accessed through this link [iSEE explorer](`r {lastProjectDigit = stringr::str_sub( sub("\\/.*", "", output$getColumn("Report")), start = -1); paste0("http://fgcz-shiny.uzh.ch/fgcz_iSEE", lastProjectDigit, "/?data=",output$getColumn("Report"),"/sce_h5")}`){target="_blank"}