Signac v0.2.4
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Analysis of Single-Cell Chromatin Data
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 and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
Readme
Signac v0.2.4
Signac is an extension of Seurat for the analysis of single-cell chromatin data.
Documentation can be found at https://satijalab.org/signac/
Install
# Install Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
install.packages("Signac")
# To install the development version
install.packages("devtools")
devtools::install_github("timoast/signac", ref = "develop")
Functions in Signac
| Name | Description | |
| FractionCountsInRegion | FractionCountsInRegion | |
| FragmentHistogram | Plot fragment length histogram | |
| ExtractCell | ExtractCell | |
| GetMotifObject | Retrieve a Motif object | |
| GetReadsInRegion | GetReadsInRegion | |
| FRiP | Calculate fraction of reads in peaks per cell | |
| IntersectMatrix | Intersect genomic coordinates with matrix rows | |
| FeatureMatrix | FeatureMatrix | |
| FilterFragments | FilterFragments | |
| Jaccard | Calculate the Jaccard index between two matrices | |
| DownsampleFeatures | DownsampleFeatures | |
| Extend | Extend | |
| GetIntersectingFeatures | Find interesecting regions between two objects | |
| blacklist_ce11 | Genomic blacklist regions for C. elegans ce11 | |
| MergeWithRegions | Region-aware object merging | |
| MatchRegionStats | Match DNA sequence characteristics | |
| NucleosomeSignal | NucleosomeSignal | |
| Motif-class | The Motif class | |
| atac_small | A small example scATAC-seq dataset | |
| MotifPlot | MotifPlot | |
| GetMotifData | Retrieve a motif matrix | |
| blacklist_ce10 | Genomic blacklist regions for C. elegans ce10 | |
| CreateMotifMatrix | CreateMotifMatrix | |
| GRangesToString | GRanges to String | |
| GenomeBinMatrix | GenomeBinMatrix | |
| StringToGRanges | String to GRanges | |
| blacklist_hg38 | Genomic blacklist regions for Human GRCh38 | |
| RegionStats | Compute base composition information for genomic ranges | |
| SetMotifData | Set motif data | |
| RunTFIDF | Compute the term-frequency inverse-document-frequency | |
| FindMotifs | FindMotifs | |
| FindTopFeatures | Find most frequently observed features | |
| SetFragments | Set the fragments file path for creating plots | |
| RunSVD | Run singular value decomposition | |
| GetFragments | GetFragments | |
| GetCellsInRegion | GetCellsInRegion | |
| TSSPlot | Plot the enrichment around TSS | |
| UnifyPeaks | Unify genomic ranges | |
| RunChromVAR | Run chromVAR | |
| blacklist_dm3 | Genomic blacklist regions for Drosophila dm3 | |
| SubsetMatrix | Subset matrix rows and columns | |
| blacklist_mm10 | Genomic blacklist regions for Mouse mm10 | |
| blacklist_dm6 | Genomic blacklist regions for Drosophila dm6 | |
| blacklist_hg19 | Genomic blacklist regions for Human hg19 | |
| TSSEnrichment | Compute TSS enrichment score per cell | |
| subset.Motif | Return a subset of a Motif object | |
| AddMotifObject | Add a Motif object to a Seurat object | |
| CutMatrix | Generate matrix of integration sites | |
| CountsInRegion | CountsInRegion | |
| CellsPerGroup | Cells per group | |
| ClosestFeature | Closest Feature | |
| SingleCoveragePlot | Plot Tn5 insertion sites over a region | |
| BinarizeCounts | Binarize counts | |
| CreateMotifObject | CreateMotifObject | |
| AverageCounts | Average Counts | |
| No Results! | ||
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Details
| Date | 2020-03-04 |
| biocViews | |
| License | MIT + file LICENSE |
| Encoding | UTF-8 |
| LazyData | true |
| RoxygenNote | 7.0.2 |
| URL | https://github.com/timoast/signac, https://satijalab.org/signac |
| BugReports | https://github.com/timoast/signac/issues |
| Collate | 'data.R' 'generics.R' 'dimension_reduction.R' 'motifs.R' 'objects.R' 'preprocessing.R' 'utilities.R' 'visualization.R' |
| NeedsCompilation | no |
| Packaged | 2020-03-04 19:15:26 UTC; stuartt |
| Repository | CRAN |
| Date/Publication | 2020-03-13 08:50:02 UTC |
| imports | BiocGenerics , Biostrings , BSgenome , data.table , dplyr , future , future.apply , GenomeInfoDb , GenomicFeatures , GenomicRanges , gggenes , ggplot2 , ggseqlogo , grid , IRanges , irlba , Matrix , patchwork , pbapply , Rsamtools , S4Vectors , Seurat , stats , tidyr , utils , zoo |
| suggests | BSgenome.Hsapiens.UCSC.hg19 , chromVAR , EnsDb.Hsapiens.v75 , JASPAR2018 , motifmatchr , SummarizedExperiment , testthat (>= 2.1.0) , TFBSTools |
| depends | methods , R (>= 3.4.0) |
| Contributors | Rahul Satija, Paul Hoffman |
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