https://github.com/bioconductor-source/signacslim
Science Score: 13.0%
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Low similarity (8.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Size: 2.39 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
SignacSlim
A slim version of Signac for developing scATAC tools using signac functions.
Why SignacSlim is developed?
Single cell ATAC-seq is a promising tool for analyzing transcriptional regulation. In addition, Seurat and Signac provides popular functions for single cell data pre-processing. However, Seurat and Signac depends on too many packages which makes them difficult for other package re-use. Signacslim is a slim version of Signac and it contains many useful methods from Signac and Seurat. SignacSlim depends less packages and can be easily installed compared with Signac and Seurat.
Demo for using SignacSlim
Generating feature matrix for >10K single cells is time-consuming in R. Using "FeatureMatrix" function provided by SignacSlim will be much faster.
``` library(SignacSlim)
fpath <- system.file("extdata", "fragments.tsv.gz", package="SignacSlim")
ppath <- system.file("extdata", "peaks.rds", package="SignacSlim")
peaks <- readRDS(ppath)
fragments <- CreateFragmentObject(fpath)
FeatureMatrix( fragments = fragments, features = peaks )
```
Note
SignacSlim only provides basic matrix level processing function as well as some quality control function.
If you have any questions about how to use SignacSlim, please see Signac and Seurat.
The copyright belongs to Tim Stuart.
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
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Dependencies
- R >= 4.1.0 depends
- Rcpp * depends
- RcppEigen * depends
- methods * depends
- BiocGenerics * imports
- GenomeInfoDb * imports
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- Rsamtools * imports
- S4Vectors * imports
- SeuratObject * imports
- biovizBase * imports
- data.table * imports
- dplyr * imports
- fastmatch * imports
- future * imports
- future.apply * imports
- ggplot2 * imports
- hdf5r * imports
- pbapply * imports
- stats * imports
- stringi * imports
- tidyr * imports
- tools * imports
- utils * imports
- knitr * suggests
- testthat * suggests