Skip to content

Commit

Permalink
Update README
Browse files Browse the repository at this point in the history
  • Loading branch information
@HDash
HDash committed Jan 3, 2025
1 parent 84b749c commit 4c9d1f6
Show file tree
Hide file tree
Showing 3 changed files with 138 additions and 25 deletions.
7 changes: 6 additions & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,12 @@ Authors@R:
family = "Skene",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-6807-3180")))
comment = c(ORCID = "0000-0002-6807-3180")),
person(given = "Hiranyamaya",
family = "Dash",
role = c("ctb"),
email = "[email protected]",
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
Expand Down
53 changes: 44 additions & 9 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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.

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

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

<details>

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

<br>
</details>
<hr>
103 changes: 88 additions & 15 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ MSTExplorer
<img src='https://github.com/neurogenomics/MSTExplorer/raw/master/inst/hex/hex.png' title='Hex sticker for MSTExplorer' height='300'><br>
[![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-1.0.0-black.svg)](https://github.com/neurogenomics/MSTExplorer)
[![](https://img.shields.io/badge/devel%20version-1.0.4-black.svg)](https://github.com/neurogenomics/MSTExplorer)
[![](https://img.shields.io/github/languages/code-size/neurogenomics/MSTExplorer.svg)](https://github.com/neurogenomics/MSTExplorer)
[![](https://img.shields.io/github/last-commit/neurogenomics/MSTExplorer.svg)](https://github.com/neurogenomics/MSTExplorer/commits/master)
<br> [![R build
Expand All @@ -12,17 +12,50 @@ status](https://github.com/neurogenomics/MSTExplorer/workflows/rworkflows/badge.
<br>
<a href='https://app.codecov.io/gh/neurogenomics/MSTExplorer/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/MSTExplorer/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>
<h4>
Authors: <i>Brian Schilder, Robert Gordon-Smith, Nathan Skene</i>
Authors: <i>Brian Schilder, Robert Gordon-Smith, Nathan Skene,
Hiranyamaya Dash</i>
</h4>
<h4>
README updated: <i>Feb-24-2024</i>
README updated: <i>Jan-03-2025</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. 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:

Expand All @@ -33,19 +66,59 @@ 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/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)
<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>

0 comments on commit 4c9d1f6

Please sign in to comment.