localizedmarkerdetector

https://github.com/klugerlab/localizedmarkerdetector

Science Score: 44.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: KlugerLab
License: other
Language: R
Default Branch: main
Size: 34.8 MB

Statistics

Stars: 0
Watchers: 4
Forks: 0
Open Issues: 0
Releases: 1

Created over 2 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

README.Rmd

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures",
  out.width = "100%"
)
```

# Localized Marker Detector




Localized Marker Detector (LMD) is a computational framework designed for the identification of gene expression markers localized to specific cell populations within single-cell RNA sequencing data. The major workflow of LMD comprises the following three main steps:

* Step1. Constructing a cell-cell affinity graph
* Step2. Diffusing the gene expression value across the cell graph
* Step3. Assigning a score to each gene based on the dynamics of its diffusion process
* Optional Downstream tasks
  * Identifying gene modules and characterizing functional cell groups
  * Cross-sample comparison

```{r pressure, echo=FALSE, out.width="100%", out.height="auto"}
knitr::include_graphics("./man/figures/LMD_workflow.png")
```

## Installation

LMD can be installed in R as follows:

``` r
install.packages("devtools")
devtools::install_github("KlugerLab/LocalizedMarkerDetector")

library("LocalizedMarkerDetector")
```

## Docker Installation

Alternatively, we provide a Docker environment with LMD and all its dependencies pre-installed. The pre-built Docker image can be downloaded using:

``` bash
docker pull ruiqi0130/lmd-rstudio:latest
```

and to run the docker container:

``` bash
docker run -it --rm --name lmd -p 8029:8787 -v /data/:/data/ docker.io/ruiqi0130/lmd-rstudio:latest
```

Here, change `/data:/data` to `:/data`. A rstudio will be on port 8029. 

## Example tutorial
Please check [LMD tutorial](https://KlugerLab.github.io/LocalizedMarkerDetector/articles/).

## References
References of LMD functions can be found [here](https://KlugerLab.github.io/LocalizedMarkerDetector/reference/index.html).

Owner

Name: Kluger Lab
Login: KlugerLab
Kind: organization

Repositories: 8
Profile: https://github.com/KlugerLab

Citation (CITATION)

citHeader("To cite the LocalizedMarkerDetector package in publications, please use the following citation:")

bibfile <- "my_paper.bib"

readLines(bibfile)

citFooter("Please also cite the package as follows:")

citEntry(
  entry = "Manual",
  title = "LocalizedMarkerDetector",
  author = personList(
    person(given = "Ruiqi", family = "Li", role = "aut"),
    person(given = "Rihao", family = "Qu", role = "aut"),
    person(given = "Francesco", family = "Strino", role = "aut")
  ),
  year = "2024",
  note = "R package version 1.0.0",
  textVersion = paste(
    "Li R, Qu R, Strino F (2024).",
    "LocalizedMarkerDetector.",
    "R package version 1.0.0."
  )
)

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