Changes in version 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. Changes in version 1.41.2 - Enhancement of plotDistToTSS(), see #241. Changes in version 1.41.1 - use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri) Changes in version 1.40.0 - Bioconductor RELEASE_3_19 (2024-05-15, Wed) Changes in version 1.38.0 - Bioconductor RELEASE_3_18 (2023-10-25, Wed) Changes in version 1.36.0 - Bioconductor RELEASE_3_17 (2023-05-03, Wed) 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)