Science Score: 49.0%
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1 of 1 committers (100.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
Last synced: 7 months ago
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JSON representation
Repository
Convert Identifiers in Biological Databases
Basic Info
- Host: GitHub
- Owner: ShixiangWang
- License: other
- Language: R
- Default Branch: master
- Size: 11.2 MB
Statistics
- Stars: 9
- Watchers: 1
- Forks: 2
- Open Issues: 4
- Releases: 0
Created over 5 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
Changelog
License
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# IDConverter
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://cran.r-project.org/package=IDConverter)
The goal of IDConverter is to convert identifiers between biological databases.
Currently, I mainly use it for promoting cancer study.
## Installation
Install the latest version of IDConverter in GitHub with:
``` r
remotes::install_github("ShixiangWang/IDConverter")
```
Or Gitee (better in China, but not updated anymore):
```r
remotes::install_git("https://gitee.com/ShixiangWang/IDConverter")
```
## Available features
**ID conversions**:
- `convert_custom()` - Convert custom database identifiers.
- `convert_icgc()` - Convert ICGC identifiers.
- `convert_pcawg()` - Convert PCAWG identifiers.
- `convert_tcga()` - Convert TCGA identifiers.
- `convert_hm_genes()` - Convert human/mouse gene IDs between Ensembl and Hugo Symbol system.
Annotation tables from [annotables](https://github.com/stephenturner/annotables) are available
in this package, you can use `ls_annotables()` to print the table list and then use
`load_data()` to download and load the data into R for conversion operation.
**Others**:
- `parse_gdc_file_uuid()` - Parse Metadata from GDC Portal File UUID.
- `filter_tcga_barcodes()` - Filter TCGA Replicate Sample Barcodes.
## Examples
```{r}
library(IDConverter)
```
To follow the CRAN policy, I have to set `tempdir()` as default data path,
however, I recommend you set the data path to a specified path with
`options(IDConverter.datapath)`.
e.g.,
```{r}
options(IDConverter.datapath = system.file("extdata", package = "IDConverter"))
```
### TCGA
```{r}
x <- convert_tcga("TCGA-02-0001-10")
x
```
### PCAWG
```{r}
x <- convert_pcawg("SP1677")
x
```
### ICGC
```{r}
x <- convert_icgc("SP29019")
x
```
### Genes
```{r}
convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")
# Or use data from annotables
ls_annotables()
grch37 = load_data("grch37")
head(grch37)
convert_custom(c("TP53", "KRAS", "EGFR", "MYC"),
from = "symbol", to = "entrez", dt = grch37)
```
## Citation
***Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy
number signature analysis tool and its application in prostate
cancer reveals distinct mutational processes and clinical outcomes.
PLoS Genet 17(5): e1009557.***
## Similar package
- [AnnoProbe](https://github.com/jmzeng1314/AnnoProbe/) ([Gitee mirror](https://gitee.com/jmzeng/annoprobe)) is an R package for transforming Chips probes to different Gene IDs.
## LICENSE
MIT\@2020, Shixiang Wang
Owner
- Name: Shixiang Wang (王诗翔)
- Login: ShixiangWang
- Kind: user
- Location: Guangzhou, China
- Company: SYSUCC
- Website: https://shixiangwang.github.io/
- Twitter: WangShxiang
- Repositories: 18
- Profile: https://github.com/ShixiangWang
纯素之道，惟神是守。守而勿失，与神为一
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| ShixiangWang | w****x@s****n | 36 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 13
- Total pull requests: 0
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 1.15
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ShixiangWang (10)
- vetmohit89 (3)
Pull Request Authors
Top Labels
Issue Labels
enhancement (4)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 236 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: IDConverter
Convert Identifiers in Biological Databases
- Homepage: https://github.com/ShixiangWang/IDConverter
- Documentation: http://cran.r-project.org/web/packages/IDConverter/IDConverter.pdf
- License: MIT + file LICENSE
- Status: removed
-
Latest release: 0.3.4
published about 3 years ago
Rankings
Forks count: 17.8%
Stargazers count: 19.8%
Average: 24.9%
Dependent repos count: 25.5%
Dependent packages count: 29.8%
Downloads: 31.7%
Maintainers (1)
Last synced:
12 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.5.0 depends
- data.table * imports
- httr * imports
- tibble * imports
- covr * suggests
- readr * suggests
- testthat * suggests