Changes in version 1.35.3
- fixed R check by removing calling BiocStyle::Biocpkg() in vignette,
instead we use yulab.utils::Biocpkg() (2023-04-11, Tue)
Changes in version 1.35.2
- fixed R check by adding 'prettydoc' to Suggests (2023-04-04, Tue)
Changes in version 1.35.1
- use ggplot to plot heatmap (2022-12-30, Fri, #203)
- update startup message to display the 'Current Protocols (2022)'
paper.
Changes in version 1.34.0
- Bioconductor RELEASE_3_16 (2022-11-02, Wed)
Changes in version 1.33.4
- add citation Q. Wang (2022) (2022-10-29, Sat)
Changes in version 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)
Changes in version 1.33.2
- supports by = "ggVennDiagram" in vennplot function (2022-09-13, Tue)
Changes in version 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)
Changes in version 1.32.0
- Bioconductor 3.15 release
Changes in version 1.31.4
- readPeakFile now supports .broadPeak and .gappedPeak files
(2021-12-17, Fri, #173)
Changes in version 1.31.3
- bug fixed of determining promoter region in minus strand
(2021-12-16, Thu, #172)
Changes in version 1.31.2
- update vignette
Changes in version 1.31.1
- bug fixed to take strand information (2021-11-10, Wed, #167)
Changes in version 1.30.0
- Bioconductor 3.14 release
Changes in version 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)
Changes in version 1.29.1
- add example for seq2gene function (2021-05-21, Fri)
Changes in version 1.28.0
- Bioconductor 3.13 release (2021-05-20, Thu)
Changes in version 1.27.5
- update GEO data (103398/1973025 GSM) (2021-05-14, Fri)
Changes in version 1.27.4
- bug fixed in determine downstream gene (2021-04-27, Thu)
- https://github.com/YuLab-SMU/ChIPseeker/pull/148
- getBioRegion now supports '3UTR' and '5UTR' (2021-03-30, Tue)
- https://github.com/YuLab-SMU/ChIPseeker/pull/146
Changes in version 1.27.3
- add two parameter, cex and radius, to plotAnnoPie (2021-03-12, Fri)
- https://github.com/YuLab-SMU/ChIPseeker/pull/144
Changes in version 1.27.2
- bug fixed of getGenomicAnnotation (2021-03-03, Wed)
- https://github.com/YuLab-SMU/ChIPseeker/issues/142
Changes in version 1.27.1
- Add support for EnsDb annotation databases in annotatePeak.
- https://github.com/YuLab-SMU/ChIPseeker/pull/120
Changes in version 1.26.0
- Bioconductor 3.12 release (2020-10-28, Wed)
Changes in version 1.23.1
- update GEO data (51079/762820 GSM) (2019-12-20, Fri)
Changes in version 1.22.0
- Bioconductor 3.10 release
Changes in version 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)
Changes in version 1.20.0
- Bioconductor 3.9 release
Changes in version 1.19.1
- add origin_label = "TSS" parameter to plotAvgProf (2018-12-12, Wed)
- https://github.com/GuangchuangYu/ChIPseeker/issues/91
Changes in version 1.18.0
- Bioconductor 3.8 release
Changes in version 1.17.2
- add flip_minor_strand parameter in getTagMatrix (2018-08-10, Fri)
- should set to FALSE if windows if not symetric
Changes in version 1.17.1
- fixed issue of vennpie by adding pseudo-count +1 (2018-07-21, Sat)
- https://www.biostars.org/p/326456/
Changes in version 1.16.0
- Bioconductor 3.7 release
Changes in version 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>
- https://github.com/GuangchuangYu/ChIPseeker/issues/76
- plotAnnoBar now visualize barplot according to the order of input
list (y-axis) (2018-02-27, Tue)
- https://github.com/GuangchuangYu/ChIPseeker/issues/73
- follow renaming of RangesList class -> IntegerRangesList in IRanges
v2.13.12
- https://github.com/GuangchuangYu/ChIPseeker/commit/b62d7922fb61e58620bbb685e4def4fb863c8e81
Changes in version 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)