From 64dd4fb08a9544c88b6ba4454bb97b8b1b56d231 Mon Sep 17 00:00:00 2001 From: igor <6363505+igordot@users.noreply.github.com> Date: Mon, 25 Jan 2021 20:24:26 -0500 Subject: [PATCH] Prepare for CRAN release --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- R/enrichment.R | 6 +++--- README.md | 2 +- cran-comments.md | 5 ++--- man/clustermole_enrichment.Rd | 6 +++--- 6 files changed, 12 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4efb13a..3f643d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: clustermole Title: Unbiased Single-Cell Transcriptomic Data Cell Type Identification -Version: 1.0.1.9001 +Version: 1.1.0 Authors@R: person(given = "Igor", family = "Dolgalev", @@ -9,7 +9,7 @@ Authors@R: email = "igor.dolgalev@nyumc.org") Description: Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases. License: MIT + file LICENSE -URL: https://igordot.github.io/clustermole, https://github.com/igordot/clustermole +URL: https://igordot.github.io/clustermole/, https://github.com/igordot/clustermole BugReports: https://github.com/igordot/clustermole/issues Depends: R (>= 3.6) diff --git a/NEWS.md b/NEWS.md index 383047f..bbf47fd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# clustermole (development version) +# clustermole 1.1.0 * Added singscore enrichment method. * Added combined enrichment method. diff --git a/R/enrichment.R b/R/enrichment.R index 83f75cf..3e89df7 100644 --- a/R/enrichment.R +++ b/R/enrichment.R @@ -9,11 +9,11 @@ #' @return A data frame of enrichment results. #' #' @references -#' Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. \emph{Nature} 462, 108–112 (2009). \url{https://doi.org/10.1038/nature08460} +#' Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. \emph{Nature} 462, 108–112 (2009). \doi{10.1038/nature08460} #' -#' Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. \emph{BMC Bioinformatics} 14, 7 (2013). \url{https://doi.org/10.1186/1471-2105-14-7} +#' Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. \emph{BMC Bioinformatics} 14, 7 (2013). \doi{10.1186/1471-2105-14-7} #' -#' Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. \emph{BMC Bioinformatics} 19, 404 (2018). \url{https://doi.org/10.1186/s12859-018-2435-4} +#' Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. \emph{BMC Bioinformatics} 19, 404 (2018). \doi{10.1186/s12859-018-2435-4} #' #' @import methods #' @import dplyr diff --git a/README.md b/README.md index bdc35df..5595085 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ The clustermole package provides three primary features: * cell type prediction based on marker genes * cell type prediction based on the full expression matrix -Check the [documentation website](https://igordot.github.io/clustermole) for more information. +Check the [documentation website](https://igordot.github.io/clustermole/) for more information. --- diff --git a/cran-comments.md b/cran-comments.md index 2822339..e3e22a0 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,8 @@ ## Test environments -* local OS X install, R 3.6.1 -* travis-ci: R 3.4, R-release, R-devel +* local OS X install, R 4.0.3 +* travis-ci: R 3.6, R-release, R-devel * win-builder: R-devel -* rchk: unbuntu-rchk platform on R-hub ## R CMD check results diff --git a/man/clustermole_enrichment.Rd b/man/clustermole_enrichment.Rd index d82ab58..cbd48f0 100644 --- a/man/clustermole_enrichment.Rd +++ b/man/clustermole_enrichment.Rd @@ -23,9 +23,9 @@ Perform enrichment of cell type signatures based on the full gene expression mat # my_enrichment <- clustermole_enrichment(expr_mat = my_expr_mat, species = "hs") } \references{ -Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. \emph{Nature} 462, 108–112 (2009). \url{https://doi.org/10.1038/nature08460} +Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. \emph{Nature} 462, 108–112 (2009). \doi{10.1038/nature08460} -Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. \emph{BMC Bioinformatics} 14, 7 (2013). \url{https://doi.org/10.1186/1471-2105-14-7} +Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. \emph{BMC Bioinformatics} 14, 7 (2013). \doi{10.1186/1471-2105-14-7} -Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. \emph{BMC Bioinformatics} 19, 404 (2018). \url{https://doi.org/10.1186/s12859-018-2435-4} +Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. \emph{BMC Bioinformatics} 19, 404 (2018). \doi{10.1186/s12859-018-2435-4} }