updated documentation from v1.0.0

NAMESPACE

@@ -1,19 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
-export(annotateBarcodeReads)
+export(aggregateBarcodes)
 export(calcDivIndexes)
 export(calcPercentileBarcodes)
 export(calcReplicateCorr)
 export(cluster_cormat)
 export(collapseReplicates)
 export(compareAbundance)
-export(countBarcodeReads)
-export(extractBAM)
-export(extractBarcodeReads)
-export(extractFASTQ)
+export(filterBarcodes)
 export(getDominantBarcodes)
 export(get_upper_tri)
-export(mapBarcodeReads)
 export(normaliseCounts)
 export(plotAbundanceLines)
 export(plotBARtabFilterQC)
@@ -29,14 +25,26 @@ export(plotBarcodeHistogram)
 export(plotBarcodePCA)
 export(plotBarcodeRegression)
 export(plotBarcodeTimeseries)
+export(plotBarcodesPerCell)
+export(plotCellsInClusters)
+export(plotCellsPerGroup)
+export(plotClusterEnrichment)
 export(plotDetectedBarcodes)
+export(plotDivIndexes)
 export(plotLibraryCumSum)
 export(plotLibraryDiversity)
+export(plotMetrics)
 export(plotOrderedBubble)
 export(plotReadCounts)
+export(plotSampleCumSum)
+export(plotUmiFilterThresholds)
+export(plotUmiPerBarcode)
 export(processBarcodeLibrary)
+export(readBartabCounts)
 export(thresholdCounts)
 import(edgeR)
 import(ggplot2)
 importFrom(ineq,Gini)
+importFrom(magrittr,"%>%")
+importFrom(rlang,.data)
 importFrom(vegan,diversity)

README.Rmd

@@ -0,0 +1,68 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/",
+  out.width = "100%"
+)
+```
+
+# bartools
+
+#### Tools for the analysis of cellular barcoding datasets
+
+<img src="man/figures/bartools_logo.png" align="right" width="260"/>
+
+### Introduction
+
+Cellular barcoding is a powerful and widespread method to accurately track the progeny of individual cells within a population, enabling the dissection of biological phenomena at single-cell resolution. However there remains a need for scalable and standardised open-source tools to pre-process and visualise cellular barcoding datasets. The `bartools` package is an R-based toolkit for the analysis of cellular barcoding information from high throughput sequencing datasets. The package consists of a suite of functions to annotate, analyse and plot DNA barcodes that are read out using common high throughput sequencing methodologies such as from Illumina machines, and also contains functions to analyse single cell expressed cellular barcoding datatsets. The `bartools` package is optimised for use with [SPLINTR](https://www.nature.com/articles/s41586-021-04206-7) lineage barcode libraries however the functions within can be adapted to any cellular barcoding methodology that utiilses random DNA barcodes.
+
+<!-- badges: start -->
+
+<!-- badges: end -->
+
+------------------------------------------------------------------------
+
+### Installation
+
+You can install `bartools` from [GitHub](https://github.com/):
+
+```{r, eval=FALSE}
+# first install dependencies from Bioconductor
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("edgeR", "limma", "ComplexHeatmap")
+
+# then install bartools from GitHub
+if (!requireNamespace("devtools", quietly = TRUE)) {
+  install.packages("devtools")
+}
+
+devtools::install_github("DaneVass/bartools", dependencies = TRUE, type = "source")
+```
+
+### Getting started
+
+See the vignettes for more details and usage examples:
+
+-   The [quickstart vignette](https://danevass.github.io/bartools/articles/quickstart.html) - bulk barcoding dataset QC and analysis
+
+-   The single-cell vignette - single-cell related capabilities of `bartools`
+
+### Documentation
+
+See the [Docs](https://danevass.github.io/bartools/) for full package documentation.
+
+### Looking for a dataset preprocessing pipeline?
+
+We have also developed [BARtab](https://github.com/DaneVass/BARtab), a pre-processing pipeline to automate the extraction and enumeration of barcode reads from raw sequence files. See the github for more information.
+
+### Contact
+
+The bartools package was developed by [Dane Vassiliadis](https://findanexpert.unimelb.edu.au/profile/366000-dane-vassiliadis). Please post any issues at <https://github.com/DaneVass/bartools/issues>

README.md

@@ -3,7 +3,7 @@
 
 # bartools
 
-#### Tools for the analysis of cellular barcoding datasets
+### Tools for the analysis of cellular barcoding datasets
 
 <img src="man/figures/bartools_logo.png" align="right" width="260"/>
 
@@ -31,14 +31,20 @@ cellular barcoding methodology that utiilses random DNA barcodes.
 
 ### Installation
 
-You can install the development version of bartools from
-[GitHub](https://github.com/):
+You can install bartools from
+[GitHub](https://github.com/DaneVass/bartools):
 
 ``` r
+# first install Bioconductor dependencies
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install(c("edgeR", "limma", "ComplexHeatmap"))
+
+# then install bartools via GitHub
 if (!requireNamespace("devtools", quietly = TRUE)) {
   install.packages("devtools")
 }
-devtools::install_github("DaneVass/bartools", dependencies = TRUE)
+devtools::install_github("DaneVass/bartools", dependencies = TRUE, force = TRUE)
 ```
 
 ### Getting started
@@ -59,5 +65,5 @@ barcode reads from raw sequence files. See the github for
 ### Contact
 
 The bartools package was developed by [Dane
-Vassiliadis](https://findanexpert.unimelb.edu.au/profile/366000-dane-vassiliadis).
+Vassiliadis](https://findanexpert.unimelb.edu.au/profile/366000-dane-vassiliadis) and [Henrietta Holze](https://github.com/HenriettaHolze).
 Please post any issues at <https://github.com/DaneVass/bartools/issues>