v0.4.5

.lintr

@@ -3,18 +3,21 @@ linters: with_defaults(
     assignment_linter,
     closed_curly_linter,
     commas_linter,
+    cyclocomp_linter(50),
     extraction_operator_linter,
+    function_left_parentheses_linter,
     implicit_integer_linter,
     infix_spaces_linter,
     line_length_linter(80),
     nonportable_path_linter,
     no_tab_linter,
     object_length_linter(40),
-    object_name_linter("lowerCamelCase"),
+    object_name_linter("camelCase"),
     object_usage_linter = NULL,
     open_curly_linter,
     semicolon_terminator_linter,
     pipe_continuation_linter,
+    seq_linter,
     single_quotes_linter,
     spaces_inside_linter,
     spaces_left_parentheses_linter,

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bcbioSingleCell
 Title: bcbio Single-Cell RNA-Seq
 Description: R package for bcbio single-cell RNA-seq analysis.
-Version: 0.4.4
-Date: 2018-09-09
+Version: 0.4.5
+Date: 2018-09-17
 Authors@R: c(
     person(
         given = "Michael",
@@ -54,12 +54,12 @@ LazyData: false
 Depends:
     R (>= 3.6),
     SingleCellExperiment (>= 1.6),
-    basejump (>= 0.11.14)
+    basejump (>= 0.11.15)
 Imports:
-    acidplots (>= 0.2.14),
+    acidplots (>= 0.2.16),
     bcbioBase (>= 0.6.10),
-    bioverbs (>= 0.2.9),
-    goalie (>= 0.3.7),
+    bioverbs (>= 0.2.10),
+    goalie (>= 0.3.8),
     BiocGenerics (>= 0.30),
     BiocParallel (>= 1.18),
     IRanges (>= 2.18.2),
@@ -73,7 +73,7 @@ Imports:
     methods,
     utils
 Suggests:
-    acidroxygen (>= 0.1.2),
+    acidroxygen (>= 0.1.3),
     BiocStyle (>= 2.12),
     R.utils (>= 2.9),
     knitr (>= 1.24),

NEWS.md

@@ -1,3 +1,11 @@
+## bcbioSingleCell 0.4.5 (2019-09-17)
+
+### Minor changes
+
+- Switched QC template to use `bcb_file` as main file input, similar to
+  bcbioRNASeq QC template.
+- Updated lintr config.
+
 ## bcbioSingleCell 0.4.4 (2019-09-09)
 
 ### Minor changes
@@ -318,7 +326,7 @@ removal with the `filterCells` function.
   `cellCountsPerCluster`, `cellTypesPerCluster`,
   `clusterCellCountsPerSample`, `fetchData` functions, `plotFeature`
   functions, `plotGene` functions, `plotMarker` functions, `plotPCA`,
-  plotTSNE`, `plotUMAP`.
+  `plotTSNE`, `plotUMAP`.
 - Now requiring [bcbioBase][] v0.4+ and [basejump][] v0.7+.
 
 ### Defunct functions
@@ -685,7 +693,7 @@ removal with the `filterCells` function.
 - Fixed y-axis scale for histogram geom in QC plots.
 - Prefiltering of very low quality barcodes with no UMIs or genes is now always
   applied. This helps avoid unwanted downstream errors with zero count barcodes.
-- Added boxplot geom support for `plotReadsPerCell().
+- Added boxplot geom support for `plotReadsPerCell()`.
 - `plotQC` geom argument is now more consistent across the paneled plots.
 - Fixed facet wrapping for aggregate samples in the QC plots.
 - Added `interestingGroups` support to `plotZerosVsDepth`, matching the other
@@ -953,7 +961,7 @@ removal with the `filterCells` function.
   arguments, where applicable.
 - Offloaded base `plotQuantileHeatmap` functionality into basejump, for use in
   [bcbioRNASeq][] package.
-- Added unit test data for `loadSingleCell().
+- Added unit test data for `loadSingleCell()`.
 - Added additional unit tests to improve code coverage.
 
 ## bcbioSingleCell 0.0.25 (2017-12-11)
@@ -1397,51 +1405,51 @@ removal with the `filterCells` function.
 
 - Initial draft release.
 
-[10X Genomics]: https://www.10xgenomics.com/
-[Acid Genomics]: https://acidgenomics.com/
+[10x genomics]: https://www.10xgenomics.com/
+[acid genomics]: https://acidgenomics.com/
 [acidplots]: https://acidplots.acidgenomics.com/
 [basejump]: https://basejump.acidgenomics.com/
 [bcbio]: https://bcbio-nextgen.readthedocs.io/
-[bcbioBase]: https://bioinformatics.sph.harvard.edu/bcbioBase/
-[bcbioRNASeq]: https://bioinformatics.sph.harvard.edu/bcbioRNASeq/
-[bcbioSingleCell]: https://bioinformatics.sph.harvard.edu/bcbioSingleCell/
-[BiocInstaller]: https://bioconductor.org/packages/BiocInstaller/
-[BiocManager]: https://bioconductor.org/packages/BiocManager/
-[Bioconductor]: https://bioconductor.org/
-[BiocParallel]: https://bioconductor.org/packages/BiocParallel/
-[Cell Ranger]: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
-[Chromium]: https://chromium.acidgenomics.com/
+[bcbiobase]: https://bioinformatics.sph.harvard.edu/bcbioBase/
+[bcbiornaseq]: https://bioinformatics.sph.harvard.edu/bcbioRNASeq/
+[bcbiosinglecell]: https://bioinformatics.sph.harvard.edu/bcbioSingleCell/
+[biocinstaller]: https://bioconductor.org/packages/BiocInstaller/
+[biocmanager]: https://bioconductor.org/packages/BiocManager/
+[bioconductor]: https://bioconductor.org/
+[biocparallel]: https://bioconductor.org/packages/BiocParallel/
+[cell ranger]: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
+[chromium]: https://chromium.acidgenomics.com/
 [conda]: https://conda.io/
 [covr]: https://github.com/jimhester/covr/
-[DESeq2]: https://bioconductor.org/packages/DESeq2/
+[deseq2]: https://bioconductor.org/packages/DESeq2/
 [dplyr]: https://dplyr.tidyverse.org/
-[edgeR]: https://bioconductor.org/packages/edgeR/
-[Ensembl]: https://www.ensembl.org/
+[edger]: https://bioconductor.org/packages/edgeR/
+[ensembl]: https://www.ensembl.org/
 [ensembldb]: https://bioconductor.org/packages/ensembldb/
 [ggplot2]: https://ggplot2.tidyverse.org/
-[GitHub]: https://github.com/
-[Google Sheets]: https://www.google.com/sheets/
-[inDrop]: https://1cell-bio.com/
+[github]: https://github.com/
+[google sheets]: https://www.google.com/sheets/
+[indrop]: https://1cell-bio.com/
 [lintr]: https://github.com/jimhester/lintr/
-[macOS]: https://www.apple.com/macos/
+[macos]: https://www.apple.com/macos/
 [monocle]: http://cole-trapnell-lab.github.io/monocle-release/
 [pkgdown]: https://pkgdown.r-lib.org/
 [pointillism]: https://pointillism.acidgenomics.com/
-[R Markdown]: http://rmarkdown.rstudio.com/
-[R]: https://www.r-project.org/
+[r markdown]: http://rmarkdown.rstudio.com/
+[r]: https://www.r-project.org/
 [rlang]: http://rlang.r-lib.org/
 [roxygen2]: https://cran.r-project.org/package=roxygen2
 [scater]: https://bioconductor.org/packages/scater/
 [scde]: https://bioconductor.org/packages/scde/
 [scone]: https://bioconductor.org/packages/scone/
 [scran]: https://bioconductor.org/packages/scran/
-[Seurat]: http://satijalab.org/seurat/
-[SummarizedExperiment]: https://bioconductor.org/packages/SummarizedExperiment/
-[SureCell]: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html
+[seurat]: http://satijalab.org/seurat/
+[summarizedexperiment]: https://bioconductor.org/packages/SummarizedExperiment/
+[surecell]: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html
 [testthat]: https://github.com/hadley/testthat/
 [tidyeval]: https://dplyr.tidyverse.org/articles/programming.html
 [tidyverse]: http://www.tidyverse.org/
-[Travis CI]: https://travis-ci.org/
+[travis ci]: https://travis-ci.org/
 [viridis]: https://cran.r-project.org/package=viridis
 [zinbwave]: https://bioconductor.org/packages/zinbwave/
-[zingeR]: https://github.com/statOmics/zingeR/
+[zinger]: https://github.com/statOmics/zingeR/

R/AllClasses.R

@@ -6,7 +6,7 @@
 #' cell quality control metrics.
 #'
 #' @author Michael Steinbaugh, Rory Kirchner
-#' @note Updated 2019-08-21.
+#' @note Updated 2019-09-09.
 #' @export
 setClass(
     Class = "bcbioSingleCell",

README.md

@@ -112,17 +112,17 @@ validObject(object)
 
 The papers and software cited in our workflows are available as a [shared library](https://paperpile.com/shared/C8EMxl) on [Paperpile][].
 
-[BiocManager]: https://cran.r-project.org/package=BiocManager
-[Bioconductor]: https://bioconductor.org/
-[Chromium]: https://www.10xgenomics.com/solutions/single-cell/
-[Paperpile]: https://paperpile.com/
-[R]: https://www.r-project.org/
-[SCE]: https://bioconductor.org/packages/SingleCellExperiment/
-[SureCell]: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html
 [bcbio]: https://bcbio-nextgen.readthedocs.io/
 [bcl2fastq]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
+[biocmanager]: https://cran.r-project.org/package=BiocManager
 [bioconda]: https://bioconda.github.io/
+[bioconductor]: https://bioconductor.org/
+[chromium]: https://www.10xgenomics.com/solutions/single-cell/
 [conda]: https://conda.io/
 [devtools]: https://cran.r-project.org/package=devtools
-[inDrops v3 index barcodes]: https://github.com/steinbaugh/koopa/blob/master/workflows/indrops/harvard_v3_sample_barcodes.csv
-[inDrops]: https://github.com/indrops/indrops/
+[indrops v3 index barcodes]: https://github.com/steinbaugh/koopa/blob/master/workflows/indrops/harvard_v3_sample_barcodes.csv
+[indrops]: https://github.com/indrops/indrops/
+[paperpile]: https://paperpile.com/
+[r]: https://www.r-project.org/
+[sce]: https://bioconductor.org/packages/SingleCellExperiment/
+[surecell]: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html