diff --git a/articles/MAGMA.Celltyping.html b/articles/MAGMA.Celltyping.html index 5cb076a..a301694 100644 --- a/articles/MAGMA.Celltyping.html +++ b/articles/MAGMA.Celltyping.html @@ -253,7 +253,7 @@

Merge results
 merged_results <- MAGMA.Celltyping::merge_results(
   MAGMA_results = MAGMA_results)
-
## Saving full merged results to ==> /tmp/Rtmp3Wdeca/MAGMA_celltyping./.lvl1.csv
+
## Saving full merged results to ==> /tmp/Rtmpx9JFRn/MAGMA_celltyping./.lvl1.csv
 knitr::kable(merged_results)
diff --git a/articles/docker.html b/articles/docker.html index e714abe..16b692a 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -103,23 +103,19 @@

-

DockerHub +

Installation

-

magma.celltyping is now available via DockerHub +

MAGMA.Celltyping is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.

-

Installation -

-
-

Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

-
docker pull neurogenomicslab/magma.celltyping
+
docker pull ghcr.io/neurogenomics/MAGMA.Celltyping

Once the image has been created, you can launch it with:

docker run \
   -d \
@@ -127,8 +123,8 @@ 
Method 1: via Docker
+ -p 8900:8787 \ + ghcr.io/neurogenomics/MAGMA.Celltyping

NOTES

@@ -155,16 +151,18 @@

Method 2: via SingularityIf you are using a system that does not allow Docker (as is the case for many institutional computing clusters), you can instead install Docker images via Singularity.

-
singularity pull docker://neurogenomicslab/magma.celltyping
+
singularity pull docker://ghcr.io/neurogenomics/MAGMA.Celltyping
+

For troubleshooting, see the Singularity +documentation.

-
-

Usage -

+
+
+

Usage +

Finally, launch the containerised Rstudio by entering the following -URL in any web browser: http://localhost:8787/

+URL in any web browser: http://localhost:8900/

Login using the credentials set during the Installation steps.

-

Session Info

diff --git a/news/index.html b/news/index.html index a0a690e..3847ea4 100644 --- a/news/index.html +++ b/news/index.html @@ -71,6 +71,8 @@

New features
  • Add auto-close-template: https://github.com/marketplace/actions/auto-close-issues
    • +
  • Host updated Docker container in GitHub Packages +

    • Bug fixes

    diff --git a/pkgdown.yml b/pkgdown.yml index ec3db35..fb1e9b4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,4 +5,4 @@ articles: docker: docker.html full_workflow: full_workflow.html MAGMA.Celltyping: MAGMA.Celltyping.html -last_built: 2024-10-02T20:41Z +last_built: 2024-10-02T23:02Z diff --git a/reference/calculate_conditional_celltype_associations.html b/reference/calculate_conditional_celltype_associations.html index 35b3647..4caacea 100644 --- a/reference/calculate_conditional_celltype_associations.html +++ b/reference/calculate_conditional_celltype_associations.html @@ -256,29 +256,29 @@

    Examples

    #> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> magma -#> --gene-results '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmputUTIC/file39c86eec05c7' +#> --gene-results '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpuSB8BI/file1c5d5abfb907' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> magma -#> --gene-results '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmputUTIC/file39c86eec05c7' +#> --gene-results '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpuSB8BI/file1c5d5abfb907' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level1.35UP.10DOWN.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> Mapping gene symbols in specificity_quantiles matrix to entrez IDs. #> magma -#> --gene-results '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmputUTIC/file39c88cb9537' +#> --gene-results '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpuSB8BI/file1c5d6e83fc65' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.Linear.ControlFor_oligodendrocytes' #> Reading enrichment results file into R. #> magma -#> --gene-results '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' -#> --gene-covar '/tmp/RtmputUTIC/file39c88cb9537' +#> --gene-results '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.genes.raw' +#> --gene-covar '/tmp/RtmpuSB8BI/file1c5d6e83fc65' #> --model direction=pos condition='oligodendrocytes' -#> --out '/tmp/RtmputUTIC/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.ControlFor_oligodendrocytes' +#> --out '/tmp/RtmpuSB8BI/MAGMA_Files/ieu-a-298.tsv.gz.35UP.10DOWN/ieu-a-298.tsv.gz.35UP.10DOWN.level2.35UP.10DOWN.ControlFor_oligodendrocytes' #> Reading enrichment results file into R.
    diff --git a/reference/celltype_associations_pipeline.html b/reference/celltype_associations_pipeline.html index 69afcae..32fe51d 100644 --- a/reference/celltype_associations_pipeline.html +++ b/reference/celltype_associations_pipeline.html @@ -247,7 +247,7 @@

    Examples

    #> Constructing top10% gene marker sets for 8 cell-types.#> Reading enrichment results file into R.#> Merging linear and top10% results -#> Saving results ==> /tmp/RtmputUTIC/Zeisel2015/MAGMA_celltyping.Zeisel2015.rds +#> Saving results ==> /tmp/RtmpuSB8BI/Zeisel2015/MAGMA_celltyping.Zeisel2015.rds diff --git a/reference/get_driver_genes.html b/reference/get_driver_genes.html index 493860e..71693c8 100644 --- a/reference/get_driver_genes.html +++ b/reference/get_driver_genes.html @@ -239,7 +239,7 @@

    Examples

    #> Returning MAGMA directories.magma_res <- MAGMA.Celltyping::merge_results( MAGMA.Celltyping::enrichment_results) -#> Saving full merged results to ==> /tmp/RtmputUTIC/MAGMA_celltyping./.lvl1.csv +#> Saving full merged results to ==> /tmp/RtmpuSB8BI/MAGMA_celltyping./.lvl1.csvgenesets <- MAGMA.Celltyping::get_driver_genes(ctd = ctd, magma_res = magma_res, GenesOut_dir = GenesOut_dir, diff --git a/reference/magma_tileplot.html b/reference/magma_tileplot.html index 8d7cd25..41d1669 100644 --- a/reference/magma_tileplot.html +++ b/reference/magma_tileplot.html @@ -167,7 +167,7 @@

    Examples

    #> see ?ewceData and browseVignettes('ewceData') for documentation#> loading from cachetile_res <- magma_tileplot(ctd=ctd, results=results) -#> Saving plot ==> /tmp/RtmputUTIC/MAGMA_Figures/Tileplots/CombinedRes_TilePlot_MAGMA_wtDendro_level1_.pdf +#> Saving plot ==> /tmp/RtmpuSB8BI/MAGMA_Figures/Tileplots/CombinedRes_TilePlot_MAGMA_wtDendro_level1_.pdf#> Warning: Using size for a discrete variable is not advised.#> Warning: Using size for a discrete variable is not advised. diff --git a/reference/results_heatmap.html b/reference/results_heatmap.html index ec4cb1c..263c033 100644 --- a/reference/results_heatmap.html +++ b/reference/results_heatmap.html @@ -173,7 +173,7 @@

    Value

    Examples

    MAGMA_results <- MAGMA.Celltyping::enrichment_results
 merged_results <- MAGMA.Celltyping::merge_results(MAGMA_results)
-#> Saving full merged results to ==> /tmp/RtmputUTIC/MAGMA_celltyping./.lvl1.csv
+#> Saving full merged results to ==> /tmp/RtmpuSB8BI/MAGMA_celltyping./.lvl1.csv
 heat <- MAGMA.Celltyping::results_heatmap(
     merged_results = merged_results,
     fdr_thresh = 1)