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nucleotideSubstitutionMatrix was moved from Biostrings to pwalign

Status: Open.

#127 In GreenleafLab/chromVAR;

· hpages opened on Apr 4, 2026

All motifs found to be differentially accessible

Status: Open.

#126 In GreenleafLab/chromVAR;

· sarah-chapin opened on Jul 10, 2025

Inclusion of non-human motifs

Status: Open.

#125 In GreenleafLab/chromVAR;

· sarah-chapin opened on Jun 30, 2025

getCounts on Nanopore long read data (bam)

Status: Open.

#124 In GreenleafLab/chromVAR;

· mtragin opened on May 9, 2025

ChromVAR Failure to detect ATAC count data despite the data existing.

Status: Open.

#123 In GreenleafLab/chromVAR;

· vficarrotta opened on May 1, 2025

Why is deviation z-score in chromVar does not have 0 mean and 1 variance?

Status: Open.

#122 In GreenleafLab/chromVAR;

· Yijia-Jiang opened on Feb 25, 2025

Question: paired design in bulk ATAC-seq analysis

Status: Open.

#121 In GreenleafLab/chromVAR;

· AlexBlais74 opened on Jan 28, 2025

error: no duplicates allowed in deviationsTsne

Status: Open.

#120 In GreenleafLab/chromVAR;

· o-doyle opened on Dec 1, 2024

Add support for DelayedMatrix

Status: Open.

#119 In GreenleafLab/chromVAR;

· mfansler opened on Oct 17, 2024

ChromVar installation - Apple silicon - R4.4.1

Status: Open.

#118 In GreenleafLab/chromVAR;

· cnerlov opened on Sep 30, 2024

Use "getBackgroundPeaks" and save bakgrounds as bedfiles rather than indexes

Status: Open.

#117 In GreenleafLab/chromVAR;

· giacomogrillo7 opened on Sep 17, 2024

ChromVAR on integrated dataset - suppressing batch effects ?

Status: Open.

#116 In GreenleafLab/chromVAR;

· solvi808 opened on Sep 6, 2024