Analysis of Single-Cell Chromatin Data
Access and modify sequence information for ChromatinAssay objects
Subset a Motif object
Accessible peaks
Calculate fraction of reads in peaks per cell
Add chromatin module
Add DNA sequence motif information
Quantify aggregated genome tiles
Compute allele frequencies per cell
Annotation
Get or set links information
Plot gene annotations
Convert objects to a ChromatinAssay
Average Counts
Plot data from BigWig files
Binarize counts
Call peaks
Set and get cell barcode information for a Fragment object
Set and get cell barcode information for a Fragment object
Cells per group
The ChromatinAssay class
Closest Feature
Find relationships between clonotypes
Combine genome region plots
Cicero connections to links
Convert between motif name and motif ID
Sparse matrix correlation
Count fragments
Counts in region
Coverage of a ChromatinAssay object
Genome browser
Plot Tn5 insertion frequency over a region
Create ChromatinAssay object
Create a Fragment object
Get gene coordinates
Create motif matrix
Create motif object
Scatterplot colored by point density
Plot sequencing depth correlation
Downsample Features
Plot gene expression
Extend
Feature Matrix
Filter cells from fragment file
Find clonotypes
FindMotifs
Find overlapping ranges for ChromatinAssay objects
Find most frequently observed features
Transcription factor footprinting analysis
Fraction of counts in a genomic region
The Fragment class
Plot fragment length histogram
Get the Fragment objects
Create gene activity matrix
Genome bin matrix
Get cells in a region
Get footprinting data
Get Fragment object data
Extract genomic ranges from EnsDb object
Identify mitochondrial variants
Find intersecting regions between two objects
Get genes linked to peaks
Get peaks linked to genes
Retrieve a motif matrix
Find transcriptional start sites
Access genomic ranges for ChromatinAssay objects
GRanges to String
Return the first rows of a fragment file
Compute Tn5 insertion bias
Inter-range transformations for ChromatinAssay objects
Intersect genomic coordinates with matrix rows
Calculate the Jaccard index between two matrices
Link peaks to genes
Plot linked genomic elements
Match DNA sequence characteristics
The Motif class
Count fragments surrounding motif sites
Plot DNA sequence motif
Get or set a motif information
Find the nearest range neighbors for ChromatinAssay objects
NucleosomeSignal
Plot peaks in a genomic region
Plot motif footprinting results
Read MGATK output
Objects exported from other packages
Region heatmap
Region enrichment analysis
Region plot
Compute base composition information for genomic ranges
Run chromVAR
Run singular value decomposition
Compute the term-frequency inverse-document-frequency
Set motif data
Signac: Analysis of Single-Cell Chromatin Data
Sorts cell metadata variable by similarity using hierarchical clusteri...
Split fragment file by cell identities
String to GRanges
Subset a Fragment object
Subset matrix rows and columns
Genome browser theme
Plot integration sites per cell
Compute TSS enrichment score per cell
Plot signal enrichment around TSSs
Unify genomic ranges
Update the file path for a Fragment object
Validate cells present in fragment file
Validate Fragment object
Validate hashes for Fragment object
Plot strand concordance vs. VMR
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>.
Useful links