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ChIPseeker 1.49.1

  • Fixed bug in getNearestFeatureIndicesAndDistances() where results for overlap == "all" were silently overridden by the overlap == "TSS" branch, causing the two modes to behave identically. (2026-09-07, Mon)
  • Comprehensive documentation updates for core functions (annotatePeak(), getGenomicAnnotation(), getTagMatrix() and related, readPeakFile(), seq2gene(), dplyr verb extensions, plotting functions, etc.).
  • Simplified redundant logic in seq2gene() by merging the promoter and flanking-gene extraction into a single condition (no behavior change).

ChIPseeker 1.48.0

  • Bioconductor RELEASE_3_23 (2026-04-29, Wed)

ChIPseeker 1.47.1

  • fixed issue in 'test-txdb.R' as 'TxDb.Hsapiens.UCSC.hg19.knownGene' changes its transcript ID from UCSC (e.g., uc002qsd.4) to Ensembl (e.g., ENST00000487630.1_3) (2025-11-04, Tue)

ChIPseeker 1.46.0

  • Bioconductor RELEASE_3_22 (2025-11-01, Sat)

ChIPseeker 1.45.2

  • new cache mechanism from 'yulab.utils' (2025-10-15, Wed)

ChIPseeker 1.44.0

  • Bioconductor RELEASE_3_21 (2025-04-17, Thu)

ChIPseeker 1.42.0

  • Bioconductor RELEASE_3_20 (2024-10-30, Wed)

ChIPseeker 1.41.3

  • Better covplot(). Support universal chromosome names, and keep the default order of multiple peaks when plot a list of GRanges object.
  • Robust generate_colors(). Edit the logical of decision, and can validate color code automatically.
  • Extend dplyr verbs (filter(), mutate(), arrange(), rename()) to peak (GRanges object or data.frame), see #242.

ChIPseeker 1.41.2

  • Enhancement of plotDistToTSS(), see #241.

ChIPseeker 1.41.1

  • use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)

ChIPseeker 1.40.0

  • Bioconductor RELEASE_3_19 (2024-05-15, Wed)

ChIPseeker 1.38.0

  • Bioconductor RELEASE_3_18 (2023-10-25, Wed)

ChIPseeker 1.36.0

  • Bioconductor RELEASE_3_17 (2023-05-03, Wed)

ChIPseeker 1.35.3

  • fixed R check by removing calling BiocStyle::Biocpkg() in vignette, instead we use yulab.utils::Biocpkg() (2023-04-11, Tue)

ChIPseeker 1.35.2

  • fixed R check by adding 'prettydoc' to Suggests (2023-04-04, Tue)

ChIPseeker 1.35.1

  • use ggplot to plot heatmap (2022-12-30, Fri, #203)
  • update startup message to display the 'Current Protocols (2022)' paper.

ChIPseeker 1.34.0

  • Bioconductor RELEASE_3_16 (2022-11-02, Wed)

ChIPseeker 1.33.4

  • add citation Q. Wang (2022) (2022-10-29, Sat)

ChIPseeker 1.33.3

  • allows passing user defined color to vennpie() (2022-10-20, Thu, #202, #207)
  • add columns paramter to annotatePeak() to better support passing EnsDb to annoDb (#193, #205)
  • export getAnnoStat() (#200, #204)

ChIPseeker 1.33.2

  • supports by = "ggVennDiagram" in vennplot function (2022-09-13, Tue)

ChIPseeker 1.33.1

  • plotPeakProf() allows passing GRanges object or a list of GRanges objects to TxDb parameter (2022-06-04, Sat)
  • add test files for getTagMatrix() and plotTagMatrix()
  • getBioRegion() supports UTR regions (3'UTR + 5'UTR)
  • makeBioRegionFromGranges() supports generating windoes from self-made GRanges object
  • allow specify colors in covplot() (2022-05-09, Mon, #185, #188)

ChIPseeker 1.32.0

  • Bioconductor 3.15 release

ChIPseeker 1.31.4

  • readPeakFile now supports .broadPeak and .gappedPeak files (2021-12-17, Fri, #173)

ChIPseeker 1.31.3

  • bug fixed of determining promoter region in minus strand (2021-12-16, Thu, #172)

ChIPseeker 1.31.2

  • update vignette

ChIPseeker 1.31.1

  • bug fixed to take strand information (2021-11-10, Wed, #167)

ChIPseeker 1.30.0

  • Bioconductor 3.14 release

ChIPseeker 1.29.2

  • extend functions for plotting peak profiles to support other types of bioregions (2021-10-15, Fri, @MingLi-929, #156, #160, #162, #163)

ChIPseeker 1.29.1

  • add example for seq2gene function (2021-05-21, Fri)

ChIPseeker 1.28.0

  • Bioconductor 3.13 release (2021-05-20, Thu)

ChIPseeker 1.27.5

  • update GEO data (103398/1973025 GSM) (2021-05-14, Fri)

ChIPseeker 1.27.4

  • bug fixed in determine downstream gene (2021-04-27, Thu)
  • getBioRegion now supports '3UTR' and '5UTR' (2021-03-30, Tue)

ChIPseeker 1.27.3

  • add two parameter, cex and radius, to plotAnnoPie (2021-03-12, Fri)

ChIPseeker 1.27.2

  • bug fixed of getGenomicAnnotation (2021-03-03, Wed)

ChIPseeker 1.27.1

  • Add support for EnsDb annotation databases in annotatePeak.

ChIPseeker 1.26.0

  • Bioconductor 3.12 release (2020-10-28, Wed)

ChIPseeker 1.23.1

  • update GEO data (51079/762820 GSM) (2019-12-20, Fri)

ChIPseeker 1.22.0

  • Bioconductor 3.10 release

ChIPseeker 1.21.1

  • new implementation of upsetplot (2019-08-29, Thu)
    • use ggupset, ggimage and ggplotify
  • subset method for csAnno object (2019-08-27, Tue)

ChIPseeker 1.20.0

  • Bioconductor 3.9 release

ChIPseeker 1.19.1

  • add origin_label = "TSS" parameter to plotAvgProf (2018-12-12, Wed)

ChIPseeker 1.18.0

  • Bioconductor 3.8 release

ChIPseeker 1.17.2

  • add flip_minor_strand parameter in getTagMatrix (2018-08-10, Fri)
    • should set to FALSE if windows if not symetric

ChIPseeker 1.17.1

ChIPseeker 1.16.0

  • Bioconductor 3.7 release

ChIPseeker 1.15.4

ChIPseeker 1.15.3