Issues

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

  deeptools/deepTools#1457 · Filter by author cindykrafft opened on Sep 5, 2026

• –regionsFileName Dear Professor

  deeptools/deepTools#1417 · Filter by author helloworldABCD1234 opened on Aug 30, 2025

• bamCoverage with DNAse-seq shift

  deeptools/deepTools#1415 · Filter by author JavierMenRev opened on Aug 22, 2025

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

  deeptools/deepTools#1409 · Filter by author lldelisle opened on Jul 8, 2025

• some blank regions show in the plotHeatmap plot

  deeptools/deepTools#1407 · Filter by author wddyzxxx opened on Jul 4, 2025

• Help interpreting these heatmaps/profiles

  deeptools/deepTools#1405 · Filter by author pterzian opened on Jun 16, 2025

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

  deeptools/deepTools#1403 · Filter by author yfZhang99 opened on May 16, 2025

• heatmap appears just dark but plot profiles look great

  deeptools/deepTools#1402 · Filter by author sahuno opened on May 9, 2025

• how to recenter diverging color scheme

  deeptools/deepTools#1400 · Filter by author jayoung opened on May 5, 2025

• Using alignmentsh can cause a bgzf_read_block error in the bam file

  deeptools/deepTools#1388 · Filter by author Zifeng0709 opened on Mar 19, 2025

• Modified-base probability plot using computeMAtrix and HeatMap

  deeptools/deepTools#1383 · Filter by author santoshbiowarrior333 opened on Feb 26, 2025

• computeMatrix to visualize DNA methylation levels

  deeptools/deepTools#1381 · Filter by author hzauyangxin opened on Feb 21, 2025

• Wondering why many sharp peaks created in the deeptools 2.0 heatmap profile

  deeptools/deepTools#1348 · Filter by author zx0223winner opened on Dec 6, 2024
  6

• Feature request: Autoscaling

  deeptools/deepTools#1338 · Filter by author dgoekbuget opened on Nov 22, 2024

• unsorted multibigwigsummary output file

  deeptools/deepTools#1337 · Filter by author mkaustav84 opened on Nov 21, 2024

• How to plot heatmap is of ATAC-seq sites at gene promoters

  deeptools/deepTools#1335 · Filter by author Krithika-Bhuvan opened on Oct 30, 2024

• Natural sort of sample labels in plotCoverage

  deeptools/deepTools#1330 · Filter by author bounlu opened on Oct 9, 2024

• Differences in DeepTools Heatmap Resolution Driven by Bed File

  deeptools/deepTools#1329 · Filter by author garrettc00per opened on Oct 8, 2024

• subset computeMatrix matrix file without computeMatrixOperations

  deeptools/deepTools#1326 · Filter by author BioLaoXu opened on Sep 27, 2024

• computeMatrix on 2 regions with replicates

  deeptools/deepTools#1318 · Filter by author asmariyaz23 opened on Jul 15, 2024

• Does alignmentSieve not support single-ended sequencing data?

  deeptools/deepTools#1317 · Filter by author li1311139481 opened on Jul 4, 2024

• How to annotate a region in Heatmap?

  deeptools/deepTools#1316 · Filter by author li1311139481 opened on Jul 4, 2024

• Clustering regions in plotHeatmap

  deeptools/deepTools#1315 · Filter by author rikrdo89 opened on Jun 14, 2024
  1

• bamCoverage [multiBamCoverage]

  deeptools/deepTools#1313 · Filter by author z5ouyang opened on May 11, 2024
  1

• RNA-seq bam to bw

  deeptools/deepTools#1310 · Filter by author Tang-pro opened on May 1, 2024