Signac

Accessible peaks

Add chromatin module

Add DNA sequence motif information

Quantify aggregated genome tiles

Compute allele frequencies per cell

Annotation

Plot gene annotations

Average Counts

Plot data from BigWig

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

Count fragments

Counts in region

Genome browser

Plot Tn5 insertion frequency over a region

Create ChromatinAssay object

Create a Fragment object

Create motif matrix

Create motif object

Plot sequencing depth correlation

Downsample Features

Plot gene expression

Extend

Calculate fraction of reads in peaks per cell

Feature Matrix

Filter cells from fragment file

Find clonotypes

FindMotifs

Find most frequently observed features

Compute fold change between two groups of cells

Transcription factor footprinting analysis

Fraction of counts in a genomic region

The Fragment class

Plot fragment length histogram

Get the Fragment objects

GRanges to String

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

Find intersecting regions between two objects

Get genes linked to peaks

Get peaks linked to genes

Retrieve a motif matrix

Find transcriptional start sites

Identify mitochondrial variants

Compute Tn5 insertion bias

Intersect genomic coordinates with matrix rows

Calculate the Jaccard index between two matrices

Link peaks to genes

Plot linked genomic elements

Get or set links information

Get gene coordinates

Match DNA sequence characteristics

The Motif class

Plot DNA sequence motif

Get or set a motif information

NucleosomeSignal

Plot peaks in a genomic region

Plot motif footprinting results

Read MGATK output

Compute base composition information for genomic ranges

Run chromVAR

Run singular value decomposition

Compute the term-frequency inverse-document-frequency

Set motif data

Split fragment file by cell identities

String to GRanges

Subset matrix rows and columns

Compute TSS enrichment score per cell

Plot signal enrichment around TSSs

Plot integration sites per cell

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

Convert objects to a ChromatinAssay

A small example scATAC-seq dataset

Genomic blacklist regions for C. elegans ce10

Genomic blacklist regions for C. elegans ce11

Genomic blacklist regions for Drosophila dm3

Genomic blacklist regions for Drosophila dm6

Genomic blacklist regions for Human hg19

Genomic blacklist regions for Human GRCh38

Unified genomic blacklist regions for Human GRCh38

Genomic blacklist regions for Mouse mm10

Coverage of a ChromatinAssay object

Find overlapping ranges for ChromatinAssay objects

Access genomic ranges for ChromatinAssay objects

Return the first rows of a fragment file

Inter-range transformations for ChromatinAssay objects

Find the nearest range neighbors for ChromatinAssay objects

Objects exported from other packages

Access and modify sequence information for ChromatinAssay objects

Subset a Motif object

Genome browser theme