add orcid and vignette

DESCRIPTION

@@ -2,7 +2,7 @@ Package: dandelionR
 Title: Single-cell Immune Repertoire Trajectory Analysis in R
 Version: 0.99.0
 Authors@R:
-    c(person(given="Jiawei", family="Yu", email = "[email protected]", role = c("aut", "cre")),
+    c(person(given="Jiawei", family="Yu", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0009-0005-9170-7881")),
       person(given="Kelvin", family="Tuong", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-6735-6808")))
 Description: dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides all the necessary tools to interface with scRepertoire and a custom implementation of absorbing markov chain for pseudotime inference, inspired based on the palantir python package.
 License: MIT + file LICENSE

README.md

@@ -1 +1,22 @@
-# dandelionR
+# dandelionR
+
+Welcome to `dandelionR`! `dandelionR` is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation in [`dandelion`](https://www.github.com/zktuong/dandelion). It provides all the necessary tools to interface with [`scRepertoire`](https://github.com/ncborcherding/scRepertoire) and a custom implementation of absorbing markov chain for pseudotime inference, inspired based on the [palantir](https://github.com/dpeerlab/Palantir) python package.
+
+## Installation
+
+You can install `dandelionR` from GitHub with:
+```{r, eval = FALSE}
+if (!requireNamespace("devtools", quietly = TRUE))
+    install.packages("devtools")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+devtools::install_github('tuonglab/dandelionR', dependencies = TRUE)
+```
+
+## Usage
+
+```{r, message = FALSE, warning = FALSE}
+library(dandelionR)
+```
+
+This is a work in progress, so please feel free to open an issue if you encounter any problems or have any suggestions for improvement.

vignettes/vignettes.rmd

@@ -0,0 +1,38 @@
+---
+title: "dandelionR"
+output: rmarkdown::html_vignette
+date: "`r Sys.Date()`"
+vignette: >
+  %\VignetteIndexEntry{dandelionR}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+# dandelionR
+
+Welcome to `dandelionR`! `dandelionR` is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation in [`dandelion`](https://www.github.com/zktuong/dandelion). It provides all the necessary tools to interface with [`scRepertoire`](https://github.com/ncborcherding/scRepertoire) and a custom implementation of absorbing markov chain for pseudotime inference, inspired based on the [palantir](https://github.com/dpeerlab/Palantir) python package.
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+    collapse = TRUE,
+    comment = "#>"
+)
+```
+
+## Installation
+
+You can install `dandelionR` from GitHub with:
+```{r, eval = FALSE}
+if (!requireNamespace("devtools", quietly = TRUE))
+    install.packages("devtools")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+devtools::install_github('tuonglab/dandelionR', dependencies = TRUE)
+```
+
+## Usage
+
+```{r, message = FALSE, warning = FALSE}
+library(dandelionR)
+```
+
+This is a work in progress, so please feel free to open an issue if you encounter any problems or have any suggestions for improvement.