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https://github.com/stephenturner/msigdf
Molecular Signatures Database (MSigDB) in a data frame
https://github.com/stephenturner/msigdf
Last synced: 6 days ago
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Molecular Signatures Database (MSigDB) in a data frame
- Host: GitHub
- URL: https://github.com/stephenturner/msigdf
- Owner: stephenturner
- Created: 2016-08-16T15:48:14.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-12-03T13:02:27.000Z (almost 6 years ago)
- Last Synced: 2023-10-26T02:12:22.675Z (about 1 year ago)
- Language: R
- Homepage: http://stephenturner.github.io/msigdf/vignettes/msigdf
- Size: 15.8 MB
- Stars: 16
- Watchers: 3
- Forks: 15
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# MSigDF
The [Molecular Signatures Database (MSigDB)](http://www.broad.mit.edu/gsea/msigdb/index.jsp) in a data frame.
Current version: [v5.2](http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_v5.2_Release_Notes) (October 2016). **For a more up-to-date version, see ToledoEM's fork at [ToledoEM/msigdf](https://github.com/ToledoEM/msigdf).**
## Installation
```r
# Install devtools if you don't already have it
install.packages("devtools")
# Just get the data
devtools::install_github("stephenturner/msigdf")
# Get the data and build the vignette (requires tidyverse, knitr, rmarkdown)
devtools::install_github("stephenturner/msigdf", build_vignettes = TRUE)
```
## Example usage
See the [package vignette](http://stephenturner.github.io/msigdf/vignettes/msigdf.html) for more.
```r
library(dplyr)
library(msigdf)
vignette("msigdf")
```
```r
msigdf.human %>%
filter(collection=="hallmark") %>%
head
```
```
collection geneset entrez
1 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 3726
2 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 2920
3 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 467
4 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 4792
5 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 7128
6 hallmark HALLMARK_TNFA_SIGNALING_VIA_NFKB 5743
```
```r
msigdf.human %>% filter(geneset=="KEGG_NON_HOMOLOGOUS_END_JOINING")
```
```
collection geneset entrez
1 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 7518
2 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 4361
3 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 27343
4 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 27434
5 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 731751
6 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 79840
7 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 3981
8 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 2237
9 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 1791
10 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 7520
11 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 10111
12 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 2547
13 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 5591
14 c2 KEGG_NON_HOMOLOGOUS_END_JOINING 64421
```
See the [package vignette](http://stephenturner.github.io/msigdf/vignettes/msigdf.html) for more.