diff --git a/DESCRIPTION b/DESCRIPTION
index 7f0590d..41c71aa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,7 +22,7 @@ Authors@R:
family = "Dash",
role = c("ctb"),
email = "hdash.work@gmail.com",
- comment = c(ORCID = "0009-0005-5514-505X")))
+ comment = c(ORCID = "0009-0005-5514-505X")))
Description: Multi-Scale Target Explorer (`MSTExplorer`) systematically identifies, prioritises,
and visualises cell-type-specific gene therapy targets across the phenome.
License: GPL-3
diff --git a/README.Rmd b/README.Rmd
index 3472b25..7d43e93 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -17,26 +17,56 @@ owner <- strsplit(URL,"/")[[1]][4]
repo <-strsplit(URL,"/")[[1]][5]
```
-## ``r pkg``: `r title`
+## Introduction
-### `r description`
-
-If you use ``r pkg``, please cite:
-
-
-> `r utils::citation(pkg)$textVersion`
+The MSTExplorer package is an extension of the
+[EWCE](https://nathanskene.github.io/EWCE/articles/EWCE.html) package. It is
+designed to run expression weighted celltype enrichment (EWCE) on multiple gene
+lists in parallel. The results are then stored both as separate .rds files, one
+for each individual EWCE analysis, as well as a in a single dataframe
+containing all the results. This package is useful in cases where you have a
+large number of related, but separate, gene lists.
## Installation
+Within R:
+
```R
if(!require("remotes")) install.packages("remotes")
remotes::install_github("`r paste(owner,repo,sep='/')`")
library(`r pkg`)
```
+
## Documentation
-### [Website](https://`r owner`.github.io/`r pkg`)
-### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
+#### [Website](https://`r owner`.github.io/`r pkg`)
+#### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
+#### [Docker/Singularity Container](https://`r owner`.github.io/`r pkg`/articles/docker.html)
+
+## Citation
+
+If you use ``r pkg``, please cite:
+
+
+> `r utils::citation(pkg)$textVersion`
+
+## Contact
+
+### [Neurogenomics Lab](https://www.neurogenomics.co.uk)
+UK Dementia Research Institute
+Department of Brain Sciences
+Faculty of Medicine
+Imperial College London
+[GitHub](https://github.com/neurogenomics)
+
+## Session Info
+
+
+
+```{r Session Info}
+utils::sessionInfo()
+```
-
+
+
diff --git a/README.md b/README.md
index 0a41d15..67fe9a5 100644
--- a/README.md
+++ b/README.md
@@ -16,14 +16,42 @@ Authors: Brian Schilder, Robert Gordon-Smith, Nathan Skene,
Hiranyamaya Dash
-README updated: Dec-16-2024
+README updated: Jan-06-2025
-## `MSTExplorer`: Multi-Scale Target Explorer
+## Introduction
-### Multi-Scale Target Explorer (`MSTExplorer`) systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.
+The MSTExplorer package is an extension of the
+[EWCE](https://nathanskene.github.io/EWCE/articles/EWCE.html) package.
+It is designed to run expression weighted celltype enrichment (EWCE) on
+multiple gene lists in parallel. The results are then stored both as
+separate .rds files, one for each individual EWCE analysis, as well as a
+in a single dataframe containing all the results. This package is useful
+in cases where you have a large number of related, but separate, gene
+lists.
+
+## Installation
+
+Within R:
+
+``` r
+if(!require("remotes")) install.packages("remotes")
+
+remotes::install_github("neurogenomics/MSTExplorer")
+library(MSTExplorer)
+```
+
+## Documentation
+
+#### [Website](https://neurogenomics.github.io/MSTExplorer)
+
+#### [Get started](https://neurogenomics.github.io/MSTExplorer/articles/MSTExplorer)
+
+#### [Docker/Singularity Container](https://neurogenomics.github.io/MSTExplorer/articles/docker.html)
+
+## Citation
If you use `MSTExplorer`, please cite:
@@ -34,19 +62,59 @@ If you use `MSTExplorer`, please cite:
> type-specific gene targets underlying thousands of rare diseases and
> subtraits. medRxiv,
-## Installation
+## Contact
-``` r
-if(!require("remotes")) install.packages("remotes")
+### [Neurogenomics Lab](https://www.neurogenomics.co.uk)
-remotes::install_github("neurogenomics/MSTExplorer")
-library(MSTExplorer)
-```
+UK Dementia Research Institute
+Department of Brain Sciences
+Faculty of Medicine
+Imperial College London
+[GitHub](https://github.com/neurogenomics)
-## Documentation
+## Session Info
-### [Website](https://neurogenomics.github.io/MSTExplorer)
+
-### [Get started](https://neurogenomics.github.io/MSTExplorer/articles/MSTExplorer)
+``` r
+utils::sessionInfo()
+```
-
+ ## R version 4.4.2 (2024-10-31)
+ ## Platform: aarch64-apple-darwin20
+ ## Running under: macOS Sequoia 15.2
+ ##
+ ## Matrix products: default
+ ## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
+ ## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
+ ##
+ ## locale:
+ ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
+ ##
+ ## time zone: Europe/London
+ ## tzcode source: internal
+ ##
+ ## attached base packages:
+ ## [1] stats graphics grDevices utils datasets methods base
+ ##
+ ## loaded via a namespace (and not attached):
+ ## [1] gtable_0.3.6 jsonlite_1.8.9 renv_1.0.11
+ ## [4] dplyr_1.1.4 compiler_4.4.2 BiocManager_1.30.25
+ ## [7] tidyselect_1.2.1 rvcheck_0.2.1 scales_1.3.0
+ ## [10] yaml_2.3.10 fastmap_1.2.0 here_1.0.1
+ ## [13] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
+ ## [16] knitr_1.49 yulab.utils_0.1.8 tibble_3.2.1
+ ## [19] desc_1.4.3 dlstats_0.1.7 rprojroot_2.0.4
+ ## [22] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3
+ ## [25] rlang_1.1.4 utf8_1.2.4 badger_0.2.4
+ ## [28] xfun_0.49 fs_1.6.5 cli_3.6.3
+ ## [31] magrittr_2.0.3 rworkflows_1.0.3 digest_0.6.37
+ ## [34] grid_4.4.2 rstudioapi_0.17.1 lifecycle_1.0.4
+ ## [37] vctrs_0.6.5 evaluate_1.0.1 glue_1.8.0
+ ## [40] data.table_1.16.2 fansi_1.0.6 colorspace_2.1-1
+ ## [43] rmarkdown_2.29 tools_4.4.2 pkgconfig_2.0.3
+ ## [46] htmltools_0.5.8.1
+
+
+
+