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TimothySundell merged 1 commit into from
Apr 23, 2026
Merged

added pak as recommended installation #1

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38 changes: 21 additions & 17 deletions README.Rmd
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Expand Up @@ -13,45 +13,49 @@ knitr::opts_chunk$set(
)
```

# TS - A collection of QoL functions <a href="https://github.com/TimothySundell/TS"><img src="man/figures/TS_logo_DALL-E_no_background.png" align="right" height="138" /></a>
# TS - A collection of QoL functions <a href="https://github.com/TimothySundell/TS"><img src="man/figures/TS_logo_DALL-E_no_background.png" align="right" height="138"/></a>

<!-- badges: start -->
`r badger::badge_lifecycle("stable")`
`r badger::badge_repostatus("Active")`
`r badger::badge_code_size("TimothySundell/TS")`
`r badger::badge_doi("10.1093/bfgp/elac044", "green")`

`r badger::badge_lifecycle("stable")` `r badger::badge_repostatus("Active")` `r badger::badge_code_size("TimothySundell/TS")` `r badger::badge_doi("10.1093/bfgp/elac044", "green")`

<!-- badges: end -->

TS was written to improve the quality of life for its creator, maybe it can help you as well?

It contains a collection of functions that may be relevant people analysing single-cell RNA-sequencing data, and analysing Ig(BCR)/TCR-sequences.
It contains a collection of functions that may be relevant people analysing single-cell RNA-sequencing data, and analysing Ig(BCR)/TCR-sequences.

**Please** give our method article a look at the **DOI** button above.
It shows the importance of removing BCR/TCR genes prior to performing unsupervised clustering and downstream analyses of scRNA-seq data containing lymphocytes.
**Please** give our method article a look at the **DOI** button above. It shows the importance of removing BCR/TCR genes prior to performing unsupervised clustering and downstream analyses of scRNA-seq data containing lymphocytes.

You can find a reference webpage [*here*](https://timothysundell.github.io/TS/), or under the *About* section in the top right corner of this webpage.

***
------------------------------------------------------------------------

## Installation

To install the latest version of the TS package:

Pak (recommended)

``` r
pak::pkg_install("TimothySundell/TS")
```

Devtools

``` r
devtools::install_github("TimothySundell/TS")
```

***
------------------------------------------------------------------------

## Comments from the author

My plan is to keep this repository updated as much as possible.
If something is not working, please post in the *Issues* section.
My plan is to keep this repository updated as much as possible. If something is not working, please post in the *Issues* section.

As of now, the package does not pass *R CMD CHECK* as the tidyverse way of coding leaves me a lot of unlinked global variables to reference.
Will maybe be fixed in the future.
As of now, the package does not pass *R CMD CHECK* as the tidyverse way of coding leaves me a lot of unlinked global variables to reference. Will maybe be fixed in the future.

***
------------------------------------------------------------------------

## The TS collection of functions can be divided into 4 main categories:

Expand All @@ -60,8 +64,8 @@ Will maybe be fixed in the future.
- Functions for analysing scRNA-seq data
- General data-wrangling

***
------------------------------------------------------------------------

## Repo activity
![Repo activity](https://repobeats.axiom.co/api/embed/6ceecc56e6072d87a2a5cba22d6ddb12968a964d.svg "Repobeats analytics image")

![Repo activity](https://repobeats.axiom.co/api/embed/6ceecc56e6072d87a2a5cba22d6ddb12968a964d.svg "Repobeats analytics image")
11 changes: 10 additions & 1 deletion README.md
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@@ -1,7 +1,7 @@

<!-- README.md is generated from README.Rmd. Please edit that file -->

# TS - A collection of QoL functions <a href="https://github.com/TimothySundell/TS"><img src="man/figures/TS_logo_DALL-E_no_background.png" align="right" height="138" /></a>
# TS - A collection of QoL functions <a href="https://github.com/TimothySundell/TS"><img src="man/figures/TS_logo_DALL-E_no_background.png" align="right" height="138"/></a>

<!-- badges: start -->

Expand All @@ -11,6 +11,7 @@ state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![](https://img.shields.io/github/languages/code-size/TimothySundell/TS.svg)](https://github.com/TimothySundell/TS)
[![](https://img.shields.io/badge/doi-10.1093/bfgp/elac044-green.svg)](https://doi.org/10.1093/bfgp/elac044)

<!-- badges: end -->

TS was written to improve the quality of life for its creator, maybe it
Expand All @@ -35,6 +36,14 @@ section in the top right corner of this webpage.

To install the latest version of the TS package:

Pak (recommended)

``` r
pak::pkg_install("TimothySundell/TS")
```

Devtools

``` r
devtools::install_github("TimothySundell/TS")
```
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