https://github.com/rainoffallingstar/erebor
https://github.com/rainoffallingstar/erebor
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/rainoffallingstar/erebor
- Owner: rainoffallingstar
- License: other
- Created: 2024-03-29T12:42:41.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2024-12-16T01:51:33.000Z (over 1 year ago)
- Last Synced: 2025-05-05T14:54:10.201Z (over 1 year ago)
- Language: R
- Size: 5.91 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# erebor
The goal of erebor is to build a R6-based package for bulk RNAseq and RRBS analysis.
## Installation
You can install the development version of sell:
```{r install,eval=FALSE}
# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
pak::pak("rainoffallingstar/ereboR")
```
## Example
This is a basic example which shows you how to solve a common problem:
```{r example,eval=FALSE}
library(erebor)
## the upstream analysis of RNA-seq
BagginsClass$new(...)
## the upstream analysis of RRBS
SamwiseClass$new(...)
### root_dir 是放bam文件的目录
### 注意，这个包在运行结束后会将bam文件拷贝到processed目录
samwise <- erebor::SamwiseClass$new(root_dir = ".",
methyratio_py = "methratio.py",
gene_fa = "Genedata/hg19.fa")
# 提取甲基化位点，并转化为bismark_cov格式,
#可以指定一个装有python2.7的conda环境(如果不为NULL)
samwise$bam2methyratio(save2bismark = T,use_conda_env = "py27",
cores = 16,
mem = 100000)
## download public data from TGCA/GEO
laml <- MoriaClass$new(mine = "TCGA-LAML",Dwarf_worker = "TGCA")
#laml$download()
```