A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.
GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat (>= 3.2.0), SeuratObject, data.table, dplyr
(>= 1.0.0), future, future.apply, ggplot2, ggseqlogo, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics,
Biostrings, ggrepel, stringi, ggbio, biovizBase,
AnnotationFilter, fastmatch, lsa, RcppRoll, scales, Rcpp,
ggforce

GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat (>= 4.0.0), SeuratObject (>= 4.0.0),
data.table, dplyr (>= 1.0.0), future, future.apply, ggplot2,
ggseqlogo, irlba, pbapply, tidyr, patchwork, stats, utils,
BiocGenerics, ggrepel, stringi, fastmatch, lsa, RcppRoll,
scales, Rcpp, ggforce, qlcMatrix, grid
testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
TFBSTools, motifmatchr, BSgenome, shiny, miniUI, rtracklayer,
biovizBase, Biostrings

'RcppExports.R' 'data.R' 'differential_accessibility.R'
'generics.R' 'dimension_reduction.R' 'footprinting.R'
'fragments.R' 'genomeinfodb-methods.R' 'granges-methods.R'
'iranges-methods.R' 'links.R' 'mito.R' 'motifs.R' 'objects.R'
'peaks.R' 'preprocessing.R' 'quantification.R' 'utilities.R'
'visualization.R'

A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
'RcppExports.R' 'data.R' 'differential_accessibility.R'
'generics.R' 'dimension_reduction.R' 'footprinting.R'
'fragments.R' 'genomeinfodb-methods.R' 'granges-methods.R'
'iranges-methods.R' 'links.R' 'mito.R' 'motifs.R' 'objects.R'
'peaks.R' 'preprocessing.R' 'quantification.R' 'utilities.R'
'visualization.R' 'zzz.R'