DESCRIPTION

Package: cisTopic
Type: Package
Title: cisTopic: Probabilistic modelling of cis-regulatory topics from
        single cell epigenomics data
Version: 0.3.0
Date: 2019-12-20
Author: Carmen Bravo González-Blas
Maintainer: Carmen Bravo González-Blas <carmen.bravogonzalezblas@kuleuven.vib.be>
Description: The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as Latent Dirichlet
    Allocation (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes
    functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.4)
biocViews: GenomicRanges, rtracklayer
Imports: stats, Matrix, lda, text2vec, doSNOW, parallel, plyr,
        AUCell (>= 1.2.4), DT, fitdistrplus,
        RcisTarget (>= 1.0.2), ggplot2, data.table,
        feather, rtracklayer, GenomicRanges, S4Vectors
Suggests: Rsubread, rGREAT, ChIPseeker, scatterplot3d, plotly, destiny, Rtsne, umap,
        ComplexHeatmap, fastcluster, TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        TxDb.Dmelanogaster.UCSC.dm3.ensGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, org.Dm.eg.db, org.Hs.eg.db,
        knitr, rmarkdown, BiocStyle, tibble
VignetteBuilder: knitr
NeedsCompilation: no