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CoveragePlot not properly handling GRanges object for features

bugSomething isn't workingSomething isn't working

Status: Open.

#1970 In stuart-lab/signac;

· daniel-spies opened on Dec 4, 2025

nCount_ATAC decreases after TSSEnrichment(ATAC, fast = FALSE) for combined Seurat object (data from several samples of snATAC)

bugSomething isn't workingSomething isn't working

Status: Open.

#1962 In stuart-lab/signac;

· zyll123 opened on Oct 10, 2025

Support for Large Sparse Matrices in Signac

enhancementNew feature or requestNew feature or request

Status: Open.

#1897 In stuart-lab/signac;

· ShanshanHe-44 opened on Feb 6, 2025

Unable to subset chromatinassay by features like in vignette "Analyzing PBMC scATAC-seq" when other assays are present

bugSomething isn't workingSomething isn't working

Status: Open.

#1847 In stuart-lab/signac;

· jzw1999 opened on Nov 23, 2024

Suggestion on argument name "max.downsample" in CoveragePlot and related functions

Status: Open.

#1791 In stuart-lab/signac;

· G3N0M3 opened on Sep 29, 2024

10X multiome subsetting cancer cell line with blacklist_ratio ~ 1 for both hg38_blacklist and hg38_blacklist_unified

Status: Open.

#1741 In stuart-lab/signac;

· methornton opened on Jul 9, 2024

Footprinting issue

bugSomething isn't workingSomething isn't working

Status: Open.

#1689 In stuart-lab/signac;

· leecon30 opened on Apr 23, 2024

TSS enrichment with a region extension 2000bp

Status: Open.

#1638 In stuart-lab/signac;

· Montsecb opened on Feb 26, 2024

BPcells doesn't work with chromatin Assay

enhancementNew feature or requestNew feature or request

Status: Open.

#1507 In stuart-lab/signac;

· LucaTucciarone opened on Oct 10, 2023

Changing Fragment object annotation style

enhancementNew feature or requestNew feature or request

Status: Open.

#1370 In stuart-lab/signac;

· daccachejoe opened on Apr 4, 2023

FeatureMatrix() should count cut sites?

enhancementNew feature or requestNew feature or request

Status: Open.

#1369 In stuart-lab/signac;

· nesetozel opened on Apr 4, 2023

Error adding gene names to the differentially accessible peaks

enhancementNew feature or requestNew feature or request

Status: Open.

#1337 In stuart-lab/signac;

· KshitijDeoghar opened on Feb 14, 2023