https://github.com/bioconductor-source/venndetail
Science Score: 13.0%
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Low similarity (9.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 912 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
VennDetail
VennDetail An R package for visualizing and extracting details of multi-sets
intersection
Description
Visualizing and extracting unique (disjoint) or overlapping subsets of multiple gene datasets are a frequently performed task for bioinformatics. Although various packages and web applications are available, no R package offering functions to extract and combine details of these subsets with user datasets in data frame is available. Moreover, graphical visualization is usually limited to six or less gene datasets and a novel method is required to properly show the subset details. We have developed VennDetail, an R package to generate high-quality Venn-Pie charts and to allow extraction of subset details from input datasets.
Installation
library(devtools)
install_github("guokai8/VennDetail")
Getting started
library(VennDetail)
A <- sample(1:1000, 400, replace = FALSE)
B <- sample(1:1000, 600, replace = FALSE)
C <- sample(1:1000, 350, replace = FALSE)
D <- sample(1:1000, 550, replace = FALSE)
res <- venndetail(list(A = A, B = B, C = C, D = D))
result <- result(res)
head(result)
Software Usage
```
getSet(res, "A") # get unique elements in A
summary(res) #show overlap 'details' of all subsets
dplot(res) #make a bargraph for 'details'
dA <- data.frame(A = A, "FC" = rnorm(400))
dB <- data.frame(B = B, "FC" = rnorm(600))
dC <- data.frame(C = C, "FC" = rnorm(350))
dD <- data.frame(D = D, "FC" = rnorm(550))
getFeature(res, subset = "Shared", rlist = list(dA, dB, dC, dD),
userowname = FALSE, gind = c("A", "B", "C", "D"))
As all these four dataframes don't have row names, we set userowname to be FALSE
```
Shiny web app
VennDetail Note: Only support five input datasets now
Contact information
For any questions please contact guokai8@gmail.com
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- UpSetR * imports
- VennDiagram * imports
- dplyr * imports
- futile.logger * imports
- ggplot2 * imports
- grDevices * imports
- grid * imports
- magrittr * imports
- methods * imports
- purrr * imports
- stats * imports
- tibble * imports
- utils * imports
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat * suggests