diff --git a/DESCRIPTION b/DESCRIPTION index 5a5c9df..f388831 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.1.2.9000 -Date: 2018-10-31 +Version: 0.1.3 +Date: 2018-11-05 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index 8f8f969..860cb9e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.1.2.9000 +# phenoptrReports 0.1.3 +**2018-11-05** New features: - New RStudio Addin - "Merge cell seg files" merges inForm output from diff --git a/_pkgdown.yml b/_pkgdown.yml index 755b90b..e10fea9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -40,14 +40,16 @@ reference: desc: These functions are added to the RStudio Addins menu. Selecting one opens a GUI. contents: - - '`analysis_app`' - '`merge_addin`' + - '`consolidate_addin`' + - '`analysis_app`' - '`unmixing_quality_addin`' - - title: Consolidation - desc: These functions implement the consolidation step. + - title: Merging and Consolidation + desc: These functions implement the merge and consolidation apps. contents: - - '`merge_and_split_cell_seg_data`' - - '`merge_and_summarize_cell_seg_data`' + - '`merge_cell_seg_files`' + - '`consolidate_and_split_cell_seg_data`' + - '`consolidate_and_summarize_cell_seg_data`' - title: Calculations desc: These functions perform the calculations for an analysis. contents: diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 39abec5..9bcd8ce 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.2 + 0.1.3 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index a8e9b32..3c7de93 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.2 + 0.1.3 @@ -95,7 +95,7 @@

Analyzing inForm data

Kent Johnson

-

2018-10-28

+

2018-11-05

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 9316969..bd27aa3 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.2 + 0.1.3 @@ -95,7 +95,7 @@

Consolidating inForm data

Kent Johnson

-

2018-10-28

+

2018-11-05

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 9e9ad73..2352a10 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.2 + 0.1.3 diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index 36e8447..a9b9009 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.2 + 0.1.3 @@ -95,7 +95,7 @@

Unmixing quality report

Kent Johnson

-

2018-10-28

+

2018-11-05

Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index 047217c..1ca6386 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.2 + 0.1.3 diff --git a/docs/index.html b/docs/index.html index c30c70e..b4cad86 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.2 + 0.1.3 @@ -99,15 +99,15 @@

Introduction

phenoptrReports generates reports based on data created by Akoya Biosciences’ inForm® software.

-
+

-Unmixing quality report

-

The unmixing quality report analyzes unmixed, singleplex images to help evaluate staining and unmixing quality. This report shows crosstalk between components and highlights potential problem areas in assay development.

+Merging data from individual fields +

The “Merge cell seg files” application merges inForm data files from individual fields to create “Merge” data files. This is similar to the inForm Merge tab but does not include the ability to review and reject individual fields.

Data aggregation and reporting

-

The consolidation and analysis applications in phenoptrReports analyze cell phenotype and expression data created by inForm. They use data from multiple inForm projects to aggregate phenoype counts, density, mean expression and H-Score for each slide and tissue category in an experiment.

+

The consolidation and analysis applications in phenoptrReports use merged data files to analyze cell phenotype and expression data created by inForm. They use data from multiple inForm projects to aggregate phenoype counts, density, mean expression and H-Score for each slide and tissue category in an experiment.

For each analysis, the applications create

+
+
+

+Unmixing quality report

+

The unmixing quality report analyzes unmixed, singleplex images to help evaluate staining and unmixing quality. This report shows crosstalk between components and highlights potential problem areas in assay development.

phenoptrReports is part of the Akoya Biosciences Phenoptics™ family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.

@@ -142,10 +147,10 @@

Getting Started

-
+

-Unmixing quality report

-

For more information about the unmixing quality report, see the Unmixing quality report tutorial.

+Merging data from individual fields

+

Use the “Merge cell seg files” addin to merge inForm data from individual fields into “Merge” data files. This is similar to the function of the inForm Merge tab and should be used only when the inForm Merge is not available.

@@ -169,6 +174,11 @@

To create the finalreports, the analysis app writes and runs an R script. The script computes the aggregated statistics, writes them to an Excel workbook, and creates visualizations of the results in a Word document.

For detailed instructions and requirements, see the Analyzing inForm data tutorial.

+
+

+Unmixing quality report

+

For more information about the unmixing quality report, see the Unmixing quality report tutorial.

+
diff --git a/docs/news/index.html b/docs/news/index.html index 1c93a62..7673e7b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.2 + 0.1.3 @@ -127,6 +127,29 @@

Changelog

Source: NEWS.md +
+

+phenoptrReports 0.1.3

+

2018-11-05

+

New features:

+ +

Misc:

+ +

phenoptrReports 0.1.2

@@ -169,6 +192,7 @@

Contents

    +
  • 0.1.3
  • 0.1.2
  • 0.1.1.0
  • 0.1.0.0
    • diff --git a/docs/reference/add_tissue_category_totals.html b/docs/reference/add_tissue_category_totals.html index f3cd007..21ea0bb 100644 --- a/docs/reference/add_tissue_category_totals.html +++ b/docs/reference/add_tissue_category_totals.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.2 + 0.1.3
@@ -84,7 +84,7 @@

@@ -85,7 +85,7 @@