build site v1.0.0

DaneVass · Dec 18, 2023 · 40f2f52 · 40f2f52
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,13 @@
 Package: bartools
 Type: Package
-Title: A toolkit for the analysis and visualisation of synthetic DNA barcodes in high thorughput sequencing datasets
-Version: 0.2.5
-Authors@R: person("Dane", "Vassiliadis", email = "[email protected]",
-                  role = c("aut", "cre"))
+Title: Analysis and visualisation of synthetic DNA barcodes in high throughput sequencing datasets
+Version: 1.0.0
+Authors@R: c(person("Dane", "Vassiliadis", email = "[email protected]",
+                  role = c("aut", "cre")),
+             person("Henrietta", "Holze", email = "[email protected]",
+                  role = "aut"))
 Maintainer: Dane Vassiliadis <[email protected]>
-Description: Analysis and visualisation of synthetic DNA barcodes in high thorughput sequencing datasets.
+Description: Analysis and visualisation of synthetic DNA barcodes in high throughput sequencing datasets.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -24,10 +26,17 @@ Imports:
     scales,
     ggpubr,
     dplyr,
+    tidyr,
+    tibble,
+    tidyselect,
+    magrittr,
     forcats,
     reshape2,
     limma,
-    methods
+    methods,
+    viridis,
+    rlang,
+    RColorBrewer
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Depends:

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,12 +4,10 @@ export(aggregateBarcodes)
 export(calcDivIndexes)
 export(calcPercentileBarcodes)
 export(calcReplicateCorr)
-export(cluster_cormat)
 export(collapseReplicates)
 export(compareAbundance)
 export(filterBarcodes)
 export(getDominantBarcodes)
-export(get_upper_tri)
 export(normaliseCounts)
 export(plotAbundanceLines)
 export(plotBARtabFilterQC)
@@ -31,8 +29,6 @@ export(plotCellsPerGroup)
 export(plotClusterEnrichment)
 export(plotDetectedBarcodes)
 export(plotDivIndexes)
-export(plotLibraryCumSum)
-export(plotLibraryDiversity)
 export(plotMetrics)
 export(plotOrderedBubble)
 export(plotReadCounts)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# bartools 1.0.0
+
+- Updated function parameter inputs across whole package
+- Updated quickstart vignette, added single-cell vignette
+- Added functions aggregateBarcodes, filterBarcodes, plotUmiFilterThresholds, plotUmiPerBarcode, readBartabCounts, plotBarcodesPerCell for single-cell data and plotSampleCumSum for bulk data
+- removed deprecated plotLibraryCumSum, plotLibraryDiversity, proportionalBubbleplot
+
 # bartools 0.2.5
 
 -   Added single cell QC plotting functions plotCellsPerGroup, plotMetrics, plotClusterEnrichment, plotCellsinClusters

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html