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plotPCA (4.0.0 re-implementation): the default table and plot hold the PC scores of the first bins, not the loadings of the samples

Status: Open.

#1459 In deeptools/deepTools;

· cindykrafft opened on Sep 5, 2026

bamCompare (4.0.0 Rust backend): --operation first/second/add/mean write the log2 ratio, and reciprocal_ratio is inverted

Status: Open.

#1457 In deeptools/deepTools;

· cindykrafft opened on Sep 5, 2026

Question regarding the calculation of effective genome size for GRCh38

Status: Open.

#1426 In deeptools/deepTools;

· jqming123 opened on Mar 20, 2026

potential duplicate code

Status: Open.

#1418 In deeptools/deepTools;

· zjsyj opened on Sep 26, 2025

–regionsFileName Dear Professor

Status: Open.

#1417 In deeptools/deepTools;

· helloworldABCD1234 opened on Aug 30, 2025

bamCoverage with DNAse-seq shift

Status: Open.

#1415 In deeptools/deepTools;

· JavierMenRev opened on Aug 22, 2025

plotFingerprint results depend on BAM file order — input sorting needed

Status: Open.

#1410 In deeptools/deepTools;

· QuentinDuvertCurie opened on Jul 15, 2025

Add a param in plotHeatmap to choose the color of the summary profile

Status: Open.

#1409 In deeptools/deepTools;

· lldelisle opened on Jul 8, 2025

some blank regions show in the plotHeatmap plot

Status: Open.

#1407 In deeptools/deepTools;

· wddyzxxx opened on Jul 4, 2025

Help interpreting these heatmaps/profiles

Status: Open.

#1405 In deeptools/deepTools;

· pterzian opened on Jun 16, 2025

RPGC normalization (--normalizeUsing RPGC) is not supported with bamCompare!

Status: Open.

#1404 In deeptools/deepTools;

· ps-puneetsharma opened on May 28, 2025

The enrichment of signal values near the TSS on the sense and antisense strands

Status: Open.

#1403 In deeptools/deepTools;

· yfZhang99 opened on May 16, 2025