DESCRIPTION

Package: FigR
Type: Package
Title: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data
Version: 0.1.0
Authors@R: c(
     person("Vinay","Kartha",email= "vinay_kartha@g.harvard.edu",role = c("aut", "cre")),
     person("Jason","D. Buenrostro",role = c("aut")))
Description: This R package supports the integration of scATAC-seq and scRNA-seq data using which one can determine
    cis-regulatory elements linked to gene to define domains of regulatory chromatin (DORCs), and TF-gene associations using FigR.
    This framework is associated with (our manuscript)[https://www.sciencedirect.com/science/article/pii/S2666979X22001082] published in 2022
URL: https://buenrostrolab.github.io/FigR/
BugReports: https://github.com/buenrostrolab/FigR/issues
Imports: Matrix, SummarizedExperiment, GenomicRanges, dplyr, ggplot2, chromVAR, doParallel, doSNOW, ggrepel, ComplexHeatmap, BuenColors, pbmcapply, tibble, scales, reshape2, Rmpfr, optmatch, FNN
Depends: Matrix, SummarizedExperiment, dplyr, ggplot2, cowplot, chromVAR, motifmatchr
Suggests: BSgenome.Mmusculus.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg38, networkD3, knitr, rmarkdown, ggrastr
VignetteBuilder: knitr
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1