diff --git a/CellBarcode_logo.png b/CellBarcode_logo.png new file mode 100644 index 0000000..7098960 Binary files /dev/null and b/CellBarcode_logo.png differ diff --git a/README.md b/README.md index 247b5e7..bd657ef 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,13 @@ [![R](https://github.com/wenjie1991/scMitoMut/actions/workflows/r.yml/badge.svg)](https://github.com/wenjie1991/scMitoMut/actions/workflows/r.yml) -# The `scMitoMut` package +# The {scMitoMut} package -The [**scMitoMut**](https://github.com/wenjie1991/scMitoMut) is a R/Bioconductor Package for Mitochondrial Mutation Analysis in Single-Cell Omics Data +![scMitoMut](./CellBarcode_logo.png) + +The [**{scMitoMut}**](https://github.com/wenjie1991/scMitoMut) is a R/Bioconductor Package for lineage informative mitochondrial mutation calling in Single-Cell sequencing. + +The mitochondrial somatic mutations are promising lineage markers for single-cell sequencing data. +The {scMitoMut} package provides a comprehensive function to call the lineage informative mitochondrial mutations using beta-binomial model. # Installation @@ -15,19 +20,22 @@ install.packages("BiocManager") BiocManager::install("scMitoMut") ``` -## Install the devel version from GitHub +## Install the devel version from GitHub or Bioconductor ```r # install.packages("devtools") devtools::install_github("wenjie1991/scMitoMut", build_vignettes = TRUE) +# or +BiocManager::install("scMitoMut", version = "devel") ``` # Vignette -The vignette can be found here: [https://github.com/wenjie1991/scMitoMut/blob/main/vignettes/Analysis_colon_cancer_dataset.Rmd](). +A vignette can be found in [Bioconductor](https://www.bioconductor.org/packages/release/bioc/vignettes/scMitoMut/inst/doc/Analysis_colon_cancer_dataset.html). -You can also access the HTML version by using the R command `browseVignettes('scMitoMut')` after installing the package. +And the source code can be found [here](https://github.com/wenjie1991/scMitoMut/blob/main/vignettes/Analysis_colon_cancer_dataset.Rmd). +You can also access the vignette by the R command `browseVignettes('scMitoMut')` after installing the package. # Mini Example @@ -85,4 +93,3 @@ plot_af_coverage(x, "chrM.1227") # Contribution You are welcome to open an issue or make a pull request. -