From 4c9d1f6f245526d93fc326d87431a3d8f5fe0de9 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Fri, 3 Jan 2025 13:05:19 +0000
Subject: [PATCH 1/3] Update README
---
DESCRIPTION | 7 +++-
README.Rmd | 53 ++++++++++++++++++++++-----
README.md | 103 ++++++++++++++++++++++++++++++++++++++++++++--------
3 files changed, 138 insertions(+), 25 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 03bbc4b..c6b653a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,12 @@ Authors@R:
family = "Skene",
role = c("aut"),
email = "nathan.skene@gmail.com",
- comment = c(ORCID = "0000-0002-6807-3180")))
+ comment = c(ORCID = "0000-0002-6807-3180")),
+ person(given = "Hiranyamaya",
+ family = "Dash",
+ role = c("ctb"),
+ email = "hdash.work@gmail.com",
+ 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..3da8388 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -17,26 +17,61 @@ owner <- strsplit(URL,"/")[[1]][4]
repo <-strsplit(URL,"/")[[1]][5]
```
-## ``r pkg``: `r title`
+## Introduction
-### `r description`
-
-If you use ``r pkg``, please cite:
+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.
-
-> `r utils::citation(pkg)$textVersion`
+This package is useful in cases where you have a large number of related, but
+separate, gene lists. In this vignette we will use an example from the Human
+Phenotype Ontology (HPO). The HPO contains over 9000 clinically relevant
+phenotypes annotated with lists of genes that have been found to be associated
+with the particular phenotype.
## Installation
+Within R:
+
```R
if(!require("remotes")) install.packages("remotes")
remotes::install_github("`r paste(owner,repo,sep='/')`")
library(`r pkg`)
```
+
## Documentation
-### [Website](https://`r owner`.github.io/`r pkg`)
-### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
+#### [Website](https://`r owner`.github.io/`r pkg`)
+#### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
+#### [Docker/Singularity Container](https://`r owner`.github.io/`r pkg`/articles/docker.html)
+
+## Citation
+
+If you use ``r pkg``, please cite:
+
+
+> `r utils::citation(pkg)$textVersion`
+
+## Contact
+
+### [Neurogenomics Lab](https://www.neurogenomics.co.uk/inst/report/EpiCompare.html)
+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 949d5f0..7d5efb0 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@ MSTExplorer
[](https://cran.r-project.org/web/licenses/GPL-3)
-[](https://github.com/neurogenomics/MSTExplorer)
+[](https://github.com/neurogenomics/MSTExplorer)
[](https://github.com/neurogenomics/MSTExplorer)
[](https://github.com/neurogenomics/MSTExplorer/commits/master)
[
-Authors: Brian Schilder, Robert Gordon-Smith, Nathan Skene
+Authors: Brian Schilder, Robert Gordon-Smith, Nathan Skene,
+Hiranyamaya Dash
-README updated: Feb-24-2024
+README updated: Jan-03-2025
-## `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. In this vignette we will use an
+example from the Human Phenotype Ontology (HPO). The HPO contains over
+9000 clinically relevant phenotypes annotated with lists of genes that
+have been found to be associated with the particular phenotype.
+
+## 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:
@@ -33,19 +66,59 @@ 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/inst/report/EpiCompare.html)
-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
+
+
+
+
From 537c4e91ab2391455df82cc8de2eda93135387cc Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Fri, 3 Jan 2025 13:07:32 +0000
Subject: [PATCH 2/3] Update README
---
README.Rmd | 9 ++-------
README.md | 10 +++-------
2 files changed, 5 insertions(+), 14 deletions(-)
diff --git a/README.Rmd b/README.Rmd
index 3da8388..ee038ba 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -24,13 +24,8 @@ The MSTExplorer package is an extension of the
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. In this vignette we will use an example from the Human
-Phenotype Ontology (HPO). The HPO contains over 9000 clinically relevant
-phenotypes annotated with lists of genes that have been found to be associated
-with the particular phenotype.
+containing all the results. This package is useful in cases where you have a
+large number of related, but separate, gene lists.
## Installation
diff --git a/README.md b/README.md
index 7d5efb0..a3a26d6 100644
--- a/README.md
+++ b/README.md
@@ -28,13 +28,9 @@ The MSTExplorer package is an extension of the
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. In this vignette we will use an
-example from the Human Phenotype Ontology (HPO). The HPO contains over
-9000 clinically relevant phenotypes annotated with lists of genes that
-have been found to be associated with the particular phenotype.
+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
From 107b2b6b6bfad9cdefcc33b0aaa2e844118c4019 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Mon, 6 Jan 2025 11:00:23 +0000
Subject: [PATCH 3/3] Update lab website link
---
README.Rmd | 2 +-
README.md | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/README.Rmd b/README.Rmd
index ee038ba..7d43e93 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -53,7 +53,7 @@ If you use ``r pkg``, please cite:
## Contact
-### [Neurogenomics Lab](https://www.neurogenomics.co.uk/inst/report/EpiCompare.html)
+### [Neurogenomics Lab](https://www.neurogenomics.co.uk)
UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
diff --git a/README.md b/README.md
index a3a26d6..633a253 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ Authors: Brian Schilder, Robert Gordon-Smith, Nathan Skene,
Hiranyamaya Dash
-README updated: Jan-03-2025
+README updated: Jan-06-2025
@@ -64,7 +64,7 @@ If you use `MSTExplorer`, please cite:
## Contact
-### [Neurogenomics Lab](https://www.neurogenomics.co.uk/inst/report/EpiCompare.html)
+### [Neurogenomics Lab](https://www.neurogenomics.co.uk)
UK Dementia Research Institute
Department of Brain Sciences