NEWS.md

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)
  • #148
• getBioRegion now supports '3UTR' and '5UTR' (2021-03-30, Tue)
  • #146

ChIPseeker 1.27.3

• add two parameter, cex and radius, to plotAnnoPie (2021-03-12, Fri)
  • #144

ChIPseeker 1.27.2

• bug fixed of getGenomicAnnotation (2021-03-03, Wed)
  • #142

ChIPseeker 1.27.1

• Add support for EnsDb annotation databases in annotatePeak.
  • #120

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)
  • #91

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

• fixed issue of vennpie by adding pseudo-count +1 (2018-07-21, Sat)
  • https://www.biostars.org/p/326456/

ChIPseeker 1.16.0

• Bioconductor 3.7 release

ChIPseeker 1.15.4

• If the required input is a named list and user input a list without name, set the name automatically and throw warning msg instead of error <2018-03-14, Wed>
  • https://support.bioconductor.org/p/106903/#106936
• change plotAvgProf's default y label <2018-03-14, Wed>
  • #76
• plotAnnoBar now visualize barplot according to the order of input list (y-axis) (2018-02-27, Tue)
  • #73
• follow renaming of RangesList class -> IntegerRangesList in IRanges v2.13.12
  • https://github.com/GuangchuangYu/ChIPseeker/commit/b62d7922fb61e58620bbb685e4def4fb863c8e81

ChIPseeker 1.15.3

• options to ignore '1st exon', '1st intron', 'downstream' and promoter subcategory when summarizing result and visualization (2018-01-09, Tue)
  • https://support.bioconductor.org/p/104676/#104689
• throw msg of 'file not found and skip' when requested url is not available when downloading BED file from GEO (2017-12-28, Thu)
  • https://support.bioconductor.org/p/104491/#104507
• bug fixed of getGene (2017-12-27, Wed)