README.md

In Honchkrow/SignacSlim: The slim version of signac

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, Signac provides popular functions for single cell data pre-processing. However, 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 basic analysis methods from Signac.

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.

The copyright belongs to Tim Stuart.

Honchkrow/SignacSlim documentation built on April 9, 2022, 1:49 a.m.