DESCRIPTION

Package: MAESTRO
Type: Package
Title: Model-based Analyses of Single-cell Transcriptome and Regulome (MACS3 fork)
Version: 1.5.4
Date: 2021-03-05
Author: Chenfei Wang, Dongqing Sun, Tao Liu, Changxin Wan, Ming (Tommy) Tang, Gali Bai, Jiaojiao Zhou
Maintainer: Dongqing Sun<dongqingsun96@gmail.com>, Gali Bai<gali.bai@hotmail.com>, Tao Liu <vladimir.liu@gmail.com>
Description: MAESTRO is an intergrative analysis pipeline to support downstream analysis of single-cell RNA-seq and single-cell ATAC-seq dataset. MAESTRO provides funtion for quality control, normalization, clustering, differential gene and peak analysis, marker gene based annotation, transcription factor identification using Cistome toolkit, and intergrative analysis for scRNA-seq and scATACseq. (MACS3 fork)
URL: https://github.com/macs3-project/MAESTRO
Depends: R (>= 4.0.2)
Imports: Seurat (>= 4.0.0), Signac (>= 1.1.1), ggplot2 (>= 3.0.0), ggrepel, cowplot, Matrix (>=
         1.2.14), dplyr, png, RColorBrewer, scales, pheatmap, MAGeCKFlute, DESeq2, Gmisc,
         grid, karyoploteR, presto, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, GenomeInfoDb
Suggests: knitr, pagoda2, RCA, MAST, scABC, devtools, uwot, cisTopic, chromVAR, motifmatchr,
          SummarizedExperiment, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
          chromVARmotifs, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene,
          EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79
Remotes: github::immunogenomics/presto@7f63f9606953f8ab643809fad6eb4daea7c471d0,
	 github::hms-dbmi/pagoda2@v0.1.1,
	 github::SUwonglab/scABC@v0.1,
	 github::GreenleafLab/chromVARmotifs@38bed559c1f4770b6c91c80bf3f8ea965da26076,
	 github::gforge/Gmisc@3.0.0
VignetteBuilder: knitr
License: GPL (>=3)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
biocViews: Software, Single-cell, RNA-seq, ATAC-seq, QualityControl, Clustering,
       DifferentialExpression, DifferentialPeakCalling, TranscriptionFactorEnrichment,
       IntegrativeAnalyis, Visualization
RoxygenNote: 7.1.1