From c06532f268106fae811d98c31395eb70f53af810 Mon Sep 17 00:00:00 2001 From: Jiri Novotny Date: Fri, 6 Oct 2023 21:54:05 +0200 Subject: [PATCH] Update docs (#6) * add CITATION * add missing Rd file * add Docker CI status badge * add scdrake citation to README --- README.Rmd | 8 +++++++- README.md | 10 +++++++++- inst/CITATION | 11 +++++++++++ man/reexports.Rd | 16 ++++++++++++++++ 4 files changed, 43 insertions(+), 2 deletions(-) create mode 100644 inst/CITATION create mode 100644 man/reexports.Rd diff --git a/README.Rmd b/README.Rmd index d962e374..d17541dd 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,7 @@ knitr::opts_chunk$set( [![Pipeline diagram](https://img.shields.io/badge/Pipeline%20diagram-Show-informational)](https://github.com/bioinfocz/scdrake/blob/main/diagrams/README.md) ![License](https://img.shields.io/github/license/bioinfocz/scdrake) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![R-CMD-check-bioc](https://github.com/bioinfocz/scdrake/actions/workflows/check-bioc.yaml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/check-bioc.yaml) +[![Docker Image CI](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml) `{scdrake}` is a scalable and reproducible pipeline for secondary analysis of droplet-based single-cell RNA-seq data. `{scdrake}` is an R package built on top of the `{drake}` package, a [Make](https://www.gnu.org/software/make)-like pipeline @@ -58,6 +58,12 @@ The pipeline structure along with [diagrams](https://github.com/bioinfocz/scdrak and links to outputs is described in `vignette("pipeline_overview")` ([link](https://bioinfocz.github.io/scdrake/articles/pipeline_overview.html)). +If you use `{scdrake}` in your research, please, consider citing + +> Kubovciak J, Kolar M, Novotny J (2023). +“Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis.” *Bioinformatics Advances*, **3**(1). +[doi:10.1093/bioadv/vbad089](https://doi.org/10.1093/bioadv/vbad089). + Huge thanks go to the authors of the [Orchestrating Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/3.15/OSCA) book on whose methods and recommendations is `{scdrake}` largely based. diff --git a/README.md b/README.md index f0fdfa70..49dd2663 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,8 @@ diagram](https://img.shields.io/badge/Pipeline%20diagram-Show-informational)](ht ![License](https://img.shields.io/github/license/bioinfocz/scdrake) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![R-CMD-check-bioc](https://github.com/bioinfocz/scdrake/actions/workflows/check-bioc.yaml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/check-bioc.yaml) +[![Docker Image +CI](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml) `{scdrake}` is a scalable and reproducible pipeline for secondary analysis of droplet-based single-cell RNA-seq data. `{scdrake}` is an R @@ -63,6 +64,13 @@ The pipeline structure along with and links to outputs is described in `vignette("pipeline_overview")` ([link](https://bioinfocz.github.io/scdrake/articles/pipeline_overview.html)). +If you use `{scdrake}` in your research, please, consider citing + +> Kubovciak J, Kolar M, Novotny J (2023). “Scdrake: a reproducible and +> scalable pipeline for scRNA-seq data analysis.” *Bioinformatics +> Advances*, **3**(1). +> [doi:10.1093/bioadv/vbad089](https://doi.org/10.1093/bioadv/vbad089). + Huge thanks go to the authors of the [Orchestrating Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/3.15/OSCA) book on whose methods and recommendations is `{scdrake}` largely based. diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 00000000..8cb07bfe --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,11 @@ +bibentry( + "Article", + title = "Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis", + author = as.person(c("Jan Kubovciak", "Michal Kolar", "Jiri Novotny")), + editor = "Guoqiang Yu", + year = 2023, + journal = "Bioinformatics Advances", + volume = 3, + number = 1, + doi = "10.1093/bioadv/vbad089" +) diff --git a/man/reexports.Rd b/man/reexports.Rd new file mode 100644 index 00000000..b56e3b32 --- /dev/null +++ b/man/reexports.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\docType{import} +\name{reexports} +\alias{reexports} +\alias{guide_edge_colourbar} +\title{Objects exported from other packages} +\keyword{internal} +\description{ +These objects are imported from other packages. Follow the links +below to see their documentation. + +\describe{ + \item{ggraph}{\code{\link[ggraph]{guide_edge_colourbar}}} +}} +