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Update README
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ Authors@R:
family = "Dash",
role = c("ctb"),
email = "[email protected]",
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
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50 changes: 40 additions & 10 deletions README.Rmd
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Expand Up @@ -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:

<!-- Modify this by editing the file: inst/CITATION -->
> `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:

<!-- Modify this by editing the file: inst/CITATION -->
> `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

<details>

```{r Session Info}
utils::sessionInfo()
```

<br>
</details>
<hr>
94 changes: 81 additions & 13 deletions README.md
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Expand Up @@ -16,14 +16,42 @@ Authors: <i>Brian Schilder, Robert Gordon-Smith, Nathan Skene,
Hiranyamaya Dash</i>
</h4>
<h4>
README updated: <i>Dec-16-2024</i>
README updated: <i>Jan-06-2025</i>
</h4>

<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->

## `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:

Expand All @@ -34,19 +62,59 @@ If you use `MSTExplorer`, please cite:
> type-specific gene targets underlying thousands of rare diseases and
> subtraits. medRxiv, <https://doi.org/10.1101/2023.02.13.23285820>

## 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)
<details>

### [Get started](https://neurogenomics.github.io/MSTExplorer/articles/MSTExplorer)
``` r
utils::sessionInfo()
```

<br>
## 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

</details>

<hr>
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