diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 493db5e..705848c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -16,12 +16,11 @@ jobs: config: - {os: windows-latest, r: 'devel' } - {os: windows-latest, r: 'release' } - - {os: macOS-latest, r: 'devel' } +# - {os: macOS-latest, r: 'devel' } - {os: macOS-latest, r: 'release' } - {os: ubuntu-20.04, r: 'devel' } - {os: ubuntu-20.04, r: 'release' } - {os: ubuntu-20.04, r: 'oldrel' } - - {os: ubuntu-20.04, r: '3.3' } env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -40,7 +39,7 @@ jobs: - uses: r-lib/actions/setup-tinytex@v1 - run: | tlmgr --version - tlmgr install ae ## Needed by vignette + tlmgr install ae grfext ## Needed by vignette tlmgr list --only-installed - uses: r-lib/actions/setup-pandoc@master diff --git a/DESCRIPTION b/DESCRIPTION index db05f80..481b666 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: facets Type: Package Title: Cellular Fraction and Copy Numbers from Tumor Sequencing -Version: 0.6.2 +Version: 0.6.2-9001 Date: 2021-10-11 Author: Venkatraman E. Seshan and Ronglai Shen Maintainer: Venkatraman E. Seshan diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..7f25314 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,31 @@ +citHeader("Please cite the 'FACETS' method and 'facets' package using the following reference:") + +citEntry( + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # BibTeX entry: + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + key = "10.1093/nar/gkw520", + entry = "article", + author = "Shen, Ronglai and Seshan, Venkatraman E.", + title = "FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing", + journal = "Nucleic Acids Research", + volume = "44", + number = "16", + pages = "e131-e131", + year = "2016", + month = "06", + abstract = "Allele-specific copy number analysis (ASCN) from next generation sequencing (NGS) data can greatly extend the utility of NGS beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications. In addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of 'actionable' mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing. We developed FACETS, an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. It is a fully integrated stand-alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples. We also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.", + issn = "0305-1048", + doi = "10.1093/nar/gkw520", + url = "https://doi.org/10.1093/nar/gkw520", + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # Plain-text citation: + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + textVersion = paste( + "Ronglai Shen and Venkatraman E. Seshan,", + "FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing,", + "Nucleic Acids Research, Volume 44, Issue 16, September 2016, Page e131,", + "doi:10.1093/nar/gkw520" + ) +) diff --git a/inst/ChangeLog b/inst/ChangeLog index 8f01278..6a74bac 100644 --- a/inst/ChangeLog +++ b/inst/ChangeLog @@ -1,12 +1,13 @@ -10/11/2021: v0.6.1-9001 +06/26/2022: v0.6.2-9001 + + o Add citation(package = "facets") + +10/12/2021: v0.6.2 o reduce memory footprint of procSnps: working on rcmat directly instead of creating out counts2logROR: working directly on out (input nam now instead of mat) o added rePreProcSample to help reanalysis starting from procSample output - -10/08/2021: v0.6.1-9001 - o Register native API. o Fix partial argument and element names. diff --git a/man/facets-package.Rd b/man/facets-package.Rd index 13ac1a5..5033eea 100644 --- a/man/facets-package.Rd +++ b/man/facets-package.Rd @@ -23,6 +23,6 @@ Maintainer: \packageMaintainer{facets} \references{ Shen, R and Seshan, VE (2016). FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. - \emph{Nucleic Acids Research} \url{https://doi.org/10.1093/nar/gkw520} + \emph{Nucleic Acids Research} \doi{10.1093/nar/gkw520} } \keyword{package}