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