BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges,
IRanges, Matrix, Rsamtools, S4Vectors, Seurat, data.table,
dplyr, future, future.apply, ggplot2, ggseqlogo, irlba,
pbapply, tidyr, zoo, patchwork, Biostrings, BSgenome, gggenes,
grid, stats, utils
GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat, data.table, dplyr, future, future.apply,
ggplot2, ggseqlogo, irlba, pbapply, tidyr, zoo, patchwork,
gggenes, grid, stats, utils, BiocGenerics
GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat (>= 3.2.0), data.table, dplyr, future,
future.apply, ggplot2, ggseqlogo, irlba, pbapply, tidyr,
patchwork, grid, stats, utils, Biobase, BiocGenerics,
Biostrings, ggrepel, stringi, ggbio, biovizBase,
AnnotationFilter, fastmatch, lsa, RcppRoll, scales, Rcpp,
qvalue
GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat (>= 3.2.0), 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 (>= 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 (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 4.0.0), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, rlang, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs
GenomeInfoDb (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 4.0.0), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, rlang, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs,
lifecycle
GenomeInfoDb (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 5.0.2), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, rlang, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs,
lifecycle
GenomeInfoDb (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 5.0.2), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, rlang,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs,
lifecycle, sparseMatrixStats, RSpectra, Seqinfo
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
GenomeInfoDb, GenomicRanges, IRanges, Matrix, Rsamtools,
S4Vectors, Seurat (>= 4.0.6), 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, tidyselect
GenomeInfoDb (>= 1.29.3), GenomicRanges, IRanges, Matrix,
Rsamtools, S4Vectors, SeuratObject (>= 4.0.0), data.table,
dplyr (>= 1.0.0), future, future.apply, ggplot2, irlba,
pbapply, tidyr, patchwork, stats, utils, BiocGenerics, stringi,
fastmatch, RcppRoll, scales, Rcpp, grid, tidyselect, vctrs
testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
TFBSTools, motifmatchr, BSgenome.Hsapiens.UCSC.hg19,
EnsDb.Hsapiens.v75, JASPAR2018
testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
TFBSTools, motifmatchr, Biostrings, BSgenome
testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
TFBSTools, motifmatchr, BSgenome, shiny, miniUI
Seurat (>= 4.0.6), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, qlcMatrix, MASS
Seurat (>= 4.0.6), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, MASS
Seurat (>= 5.0.2), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, MASS
Seurat (>= 5.0.2), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, MASS, wrswoR
Seurat (>= 5.0.2), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), SummarizedExperiment, TFBSTools, motifmatchr, BSgenome,
shiny, miniUI, rtracklayer, biovizBase, Biostrings, lsa, MASS,
wrswoR, fgsea
testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
TFBSTools, motifmatchr, BSgenome, shiny, miniUI, rtracklayer,
biovizBase, Biostrings
Seurat (>= 4.0.6), ggforce, ggrepel, ggseqlogo, testthat (>=
2.1.0), chromVAR, SummarizedExperiment, TFBSTools, motifmatchr,
BSgenome, shiny, miniUI, rtracklayer, biovizBase, Biostrings,
lsa, qlcMatrix