diff --git a/README.Rmd b/README.Rmd index 46505dc..2c1015c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -10,6 +10,8 @@ editor_options: ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) +pkg <- read.dcf(file="DESCRIPTION", + fields = "Package")[[1]] ``` ## Intro @@ -44,6 +46,12 @@ Click for instructions on how to create a Docker or Singularity container with `HPOExplorer` and Rstudio pre-installed. +# Citation + +If you use ``r pkg``, please cite: + + +> `r utils::citation(pkg)$textVersion` # Session Info diff --git a/README.md b/README.md index 932a126..3c4cc0f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@
[![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) -[![](https://img.shields.io/badge/devel%20version-0.99.6-black.svg)](https://github.com/neurogenomics/HPOExplorer) +[![](https://img.shields.io/badge/devel%20version-0.99.7-black.svg)](https://github.com/neurogenomics/HPOExplorer) [![](https://img.shields.io/github/languages/code-size/neurogenomics/HPOExplorer.svg)](https://github.com/neurogenomics/HPOExplorer) [![](https://img.shields.io/github/last-commit/neurogenomics/HPOExplorer.svg)](https://github.com/neurogenomics/HPOExplorer/commits/master)
[![R build @@ -13,7 +13,7 @@ status](https://github.com/neurogenomics/HPOExplorer/workflows/rworkflows/badge. Authors: Brian Schilder, Robert Gordon-Smith, Nathan Skene

-Most recent update: Mar-07-2023 +Most recent update: Mar-31-2023

## Intro @@ -49,6 +49,17 @@ Click for instructions on how to create a Docker or Singularity container with `HPOExplorer` and Rstudio pre-installed. +# Citation + +If you use `HPOExplorer`, please cite: + + + +> Kitty B. Murphy, Robert Gordon-Smith, Jai Chapman, Momoko Otani, Brian +> M. Schilder, Nathan G. Skene (2023) Identification of cell +> type-specific gene targets underlying thousands of rare diseases and +> subtraits. medRxiv, + # Session Info
@@ -72,24 +83,35 @@ utils::sessionInfo() ## [1] stats graphics grDevices utils datasets methods base ## ## loaded via a namespace (and not attached): - ## [1] pillar_1.8.1 compiler_4.2.1 RColorBrewer_1.1-3 - ## [4] BiocManager_1.30.20 bitops_1.0-7 yulab.utils_0.0.6 - ## [7] tools_4.2.1 digest_0.6.31 jsonlite_1.8.4 - ## [10] evaluate_0.20 lifecycle_1.0.3 tibble_3.1.8 - ## [13] gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 - ## [16] graph_1.76.0 cli_3.6.0 rstudioapi_0.14 - ## [19] rvcheck_0.2.1 yaml_2.3.7 xfun_0.37 - ## [22] fastmap_1.1.0 dplyr_1.1.0 knitr_1.42 - ## [25] generics_0.1.3 desc_1.4.2 vctrs_0.5.2 - ## [28] dlstats_0.1.6 stats4_4.2.1 rprojroot_2.0.3 - ## [31] grid_4.2.1 tidyselect_1.2.0 here_1.0.1 - ## [34] Biobase_2.58.0 glue_1.6.2 R6_2.5.1 - ## [37] fansi_1.0.4 XML_3.99-0.13 RBGL_1.74.0 - ## [40] rmarkdown_2.20.1 ggplot2_3.4.1 badger_0.2.3 - ## [43] magrittr_2.0.3 BiocGenerics_0.44.0 biocViews_1.66.2 - ## [46] scales_1.2.1 htmltools_0.5.4 rworkflows_0.99.7 - ## [49] RUnit_0.4.32 colorspace_2.1-0 renv_0.17.0 - ## [52] utf8_1.2.3 RCurl_1.98-1.10 munsell_0.5.0 + ## [1] here_1.0.1 rprojroot_2.0.3 digest_0.6.31 + ## [4] utf8_1.2.3 BiocFileCache_2.6.1 R6_2.5.1 + ## [7] stats4_4.2.1 RSQLite_2.3.0 evaluate_0.20 + ## [10] httr_1.4.5 ggplot2_3.4.1 pillar_1.9.0 + ## [13] yulab.utils_0.0.6 rworkflows_0.99.8 biocViews_1.66.3 + ## [16] rlang_1.1.0 curl_5.0.0 data.table_1.14.8 + ## [19] rstudioapi_0.14 whisker_0.4.1 blob_1.2.4 + ## [22] DT_0.27 RUnit_0.4.32 rmarkdown_2.20.1 + ## [25] desc_1.4.2 readr_2.1.4 stringr_1.5.0 + ## [28] htmlwidgets_1.6.2 dlstats_0.1.6 BiocPkgTools_1.16.1 + ## [31] igraph_1.4.1 RCurl_1.98-1.10 bit_4.0.5 + ## [34] munsell_0.5.0 compiler_4.2.1 xfun_0.37 + ## [37] pkgconfig_2.0.3 BiocGenerics_0.44.0 rorcid_0.7.0 + ## [40] htmltools_0.5.4 tidyselect_1.2.0 tibble_3.2.1 + ## [43] httpcode_0.3.0 XML_3.99-0.14 fansi_1.0.4 + ## [46] dplyr_1.1.1 tzdb_0.3.0 dbplyr_2.3.2 + ## [49] bitops_1.0-7 rappdirs_0.3.3 crul_1.3 + ## [52] grid_4.2.1 RBGL_1.74.0 jsonlite_1.8.4 + ## [55] gtable_0.3.3 lifecycle_1.0.3 DBI_1.1.3 + ## [58] magrittr_2.0.3 scales_1.2.1 graph_1.76.0 + ## [61] cli_3.6.0 stringi_1.7.12 cachem_1.0.7 + ## [64] renv_0.17.2 fauxpas_0.5.0 xml2_1.3.3 + ## [67] rvcheck_0.2.1 filelock_1.0.2 generics_0.1.3 + ## [70] vctrs_0.6.1 gh_1.4.0 RColorBrewer_1.1-3 + ## [73] tools_4.2.1 bit64_4.0.5 Biobase_2.58.0 + ## [76] glue_1.6.2 hms_1.1.3 fastmap_1.1.1 + ## [79] yaml_2.3.7 colorspace_2.1-0 BiocManager_1.30.20 + ## [82] rvest_1.0.3 memoise_2.0.1 badger_0.2.3 + ## [85] knitr_1.42