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NEWS
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CHANGES IN VERSION 1.15.2
------------------------
o bug fixed for 'overlap = "all"' to consider strand information <2017-12-12, Tue>
CHANGES IN VERSION 1.15.1
------------------------
o define downstream distance via options(ChIPseeker.downstreamDistance = 3000)
+ https://support.bioconductor.org/p/103135/
CHANGES IN VERSION 1.13.1
------------------------
o fixed issue of naming intronList <2017-07-06, Thu>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/57#issuecomment-313342399
CHANGES IN VERSION 1.12.0
------------------------
o BioC 3.5 release <2017-04-26, Wed>
CHANGES IN VERSION 1.11.4
------------------------
o bug fixed of intron rank <2017-04-19, Wed>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/54
CHANGES IN VERSION 1.11.3
------------------------
o bug fixed of dropAnno <2017-04-10, Mon>
o bug fixed of peak width generated by shuffle <2017-03-31, Fri>
+ <https://github.com/GuangchuangYu/ChIPseeker/issues/51>
CHANGES IN VERSION 1.11.2
------------------------
o optimize getGeneAnno <2016-12-21, Wed>
o change plotAnnoBar and plotDistToTSS according to stacking bar order change in ggplot2 (v2.2.0) <2016-12-16, Fri>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/47
+ https://blog.rstudio.org/2016/11/14/ggplot2-2-2-0/
CHANGES IN VERSION 1.11.1
------------------------
o update startup message <2016-11-09, Wed>
CHANGES IN VERSION 1.10.0
------------------------
o BioC 3.4 released <2016-10-18, Tue>
CHANGES IN VERSION 1.9.8
------------------------
o plotAvgProf/plotAvgProf2 order of panel by names of input tagMatrix List <2016-09-25, Sun>
o test ENSEMBL ID using '^ENS' instead of '^ENSG' <2016-09-20, Tue>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/41
CHANGES IN VERSION 1.9.7
------------------------
o unit test <2016-08-16, Tue>
CHANGES IN VERSION 1.9.6
------------------------
o update vignette <2016-08-16, Tue>
CHANGES IN VERSION 1.9.5
------------------------
o when TxDb doesn't have gene_id information, converting gene ID (ensembl/entrez and symbol) will be omitted instead of throw error. <2016-08-02, Tue>
+ https://www.biostars.org/p/204142
o bug fixed if testing targetPeak is a list of GRanges objects in enrichPeakOverlap function <2016-07-20, Wed>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/37
+ https://github.com/GuangchuangYu/ChIPseeker/issues/36
o fixed typo in determine gene ID type <2016-06-21, Tue>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/28#issuecomment-227212519
o move upsetplot generics to DOSE and import from DOSE to prevent function name conflict <2016-06-14, Tue>
CHANGES IN VERSION 1.9.4
------------------------
o bug fixed <2016-06-08, Wed>
+ https://github.com/GuangchuangYu/ChIPseeker/issues/17#issuecomment-224407402
+ https://github.com/GuangchuangYu/ChIPseeker/pull/24/files
CHANGES IN VERSION 1.9.3
------------------------
o use byte compiler <2016-05-18, Wed>
o https://github.com/Bioconductor-mirror/ChIPseeker/commit/f1ada57b9c66a1a44355bbbbdaf5b0a88e10cf7d
CHANGES IN VERSION 1.9.2
------------------------
o name tagMatrix in plotAvgProf automatically if missing <2016-05-12, Thu>
o https://github.com/Bioconductor-mirror/ChIPseeker/commit/d5f16b2bc01725e30282c3acb33007ef521a514c
CHANGES IN VERSION 1.9.1
------------------------
o bug fixed in getNearestFeatureIndicesAndDistances <2016-05-11, Wed>
+ correct metadata in dummy NA feature
CHANGES IN VERSION 1.8.0
------------------------
o BioC 3.3 released <2016-05-05, Thu>
CHANGES IN VERSION 1.7.15
------------------------
o update GEO data <2016-03-21, Mon>
CHANGES IN VERSION 1.7.14
------------------------
o list_to_dataframe works with data frames that have different colnames <2016-03-10, Thu>
CHANGES IN VERSION 1.7.13
------------------------
o support annotate peaks with custom regions via passing TxDb=user_defined_GRanges to annotatePeak <2016-03-06, Sun>
CHANGES IN VERSION 1.7.12
------------------------
o fixed R check <2016-03-05, Sat>
o implement list_to_dataframe that mimic ldply and remove ldply dependency <2016-03-05, Sat>
CHANGES IN VERSION 1.7.11
------------------------
o fixed issue in testing list in covplot introduced in 1.7.9 <2016-03-02, Wed>
CHANGES IN VERSION 1.7.10
------------------------
o determined gene ID type if TxDb doesn't contain corresponding metadata <2016-03-01, Tue>
+ fixed https://github.com/GuangchuangYu/ChIPseeker/issues/28
CHANGES IN VERSION 1.7.9
------------------------
o covplot support GRangesList <2016-02-24, Wed>
o update ReactomePA citation info <2016-02-17, Wed>
CHANGES IN VERSION 1.7.8
------------------------
o fixed BUG of Peaks upstream first or downstream last gene not annotated <2016-01-20, Wed>
+ contributed by Michael Kluge
+ see https://github.com/GuangchuangYu/ChIPseeker/pull/24
CHANGES IN VERSION 1.7.7
------------------------
o bug fixed in newly introduced parameter 'overlap'. solve NA issue. <2016-01-13, Wed>
CHANGES IN VERSION 1.7.6
------------------------
o introduce 'overlap' parameter in annotatePeak, by default overlap="TSS" and only overlap with TSS will be reported as the nearest gene.
if overlap="all", then gene overlap with peak will be reported as nearest gene, no matter the overlap is at TSS region or not. <2016-01-12, Tue>
o bug fixed in find overlap with peaks have strand info. <2016-01-12, Tue>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/23
CHANGES IN VERSION 1.7.5
------------------------
o add paramters, sameStrand,ignoreOverlap, ignoreUpstream and ignoreDownstream in annotatePeak <2016-01-10, Sun>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/17
o bug fixed in peak orientation <2016-01-10, Sun>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/22
CHANGES IN VERSION 1.7.4
------------------------
o stop if input list of csAnno object has no name attribute
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/21
+ plotAnnoBar
+ plotDistToTSS
o [covplot] xlim now not only restrict the window of data but also set the limit of the graphic object <2015-12-30, Wed>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/20
CHANGES IN VERSION 1.7.3
------------------------
o fixed R check <2015-12-29, Tue>
CHANGES IN VERSION 1.7.2
------------------------
o use geom_rect instead of geom_segment in covplot <2015-11-30, Mon>
o open lower parameter (by default =1) to specific lower cutoff of coverage signal <2015-11-29, Sun>
o fixed covplot to work with None RleViews of specific chromosome <2015-11-29, Sun>
o addFlankGeneInfo now works with level="gene" <2015-11-19, Thu>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/18
CHANGES IN VERSION 1.7.1
------------------------
o fixed extracting ID type from TxDb object, since the change of metadata(TxDb). now using grep to extract. <2015-10-27, Tue>
o add vp parameter to set viewport of vennpie on top of upsetplot by user request <2015-10-26, Mon>
+ see http://ygc.name/2015/07/28/upsetplot-in-chipseeker/#comment-19470
o getBioRegion function <2015-10-20, Tue>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/16
CHANGES IN VERSION 1.7.0
------------------------
o BioC 3.3 branch
CHANGES IN VERSION 1.5.11
------------------------
o remove ellipsis parameter in enrichPeakOverlap function and extend it to support GRanges objects <2015-10-08, Thu>
+ see https://support.bioconductor.org/p/73069/
o fixed the issue, https://github.com/GuangchuangYu/ChIPseeker/issues/13 <2015-10-05, Mon>
o update GEO info, now contains >18,000 bed file information <2015-09-24, Thu>
CHANGES IN VERSION 1.5.10
------------------------
o dropAnno function, eg. drop nearest gene annotation that far from TSS (>10k). <2015-09-17, Thu>
+ see https://github.com/GuangchuangYu/ChIPseeker/issues/9
+ add parameter distanceToTSS_cutoff to enrichAnnoOverlap
o use base::subset in plotDistToTSS instead of subsetting data within geom_bar <2015-09-17, Thu>
+ see https://github.com/hadley/ggplot2/issues/1295
+ subset parameter in layer will be removed in next release of ggplot2.
CHANGES IN VERSION 1.5.9
------------------------
o bug fixed of enrichAnnoOverlap <2015-08-26, Wed>
o change parameter order.matrix to order.by in upsetplot to meet the change of UpSetR pkg <2015-08-26, Wed>
CHANGES IN VERSION 1.5.8
------------------------
o better implementation of getFirstHitIndex. <2015-07-29, Wed>
+ contributed by Herve Pages.
+ see https://support.bioconductor.org/p/70432/#70545.
CHANGES IN VERSION 1.5.7
------------------------
o add vennpie parameter in upsetplot <2015-07-20, Mon>
o upsetplot function for csAnno object <2015-07-20, Mon>
CHANGES IN VERSION 1.5.6
------------------------
o update citation info <2015-07-09, Thu>
o BED file +1 shift for BED coordinate system start at 0 <2015-07-07, Tue>
CHANGES IN VERSION 1.5.5
------------------------
o seq2gene for linking genomic regions to genes by many-to-many mapping. <2015-06-29, Mon>
CHANGES IN VERSION 1.5.4
------------------------
o add pseudocount in enrichPeakOverlap to prevent 0 pvalue <2015-05-22, Fri>
CHANGES IN VERSION 1.5.3
------------------------
o convert the vignette from Rnw to Rmd format <2015-05-17, Sun>
CHANGES IN VERSION 1.5.1
------------------------
o minor bug fixed in getChrCov <2015-04-27, Mon>
CHANGES IN VERSION 1.3.15
------------------------
o update vignette <2015-03-31, Tue>
CHANGES IN VERSION 1.3.14
------------------------
o add pool parameter in enrichPeakOverlap <2015-03-30, Mon>
CHANGES IN VERSION 1.3.13
------------------------
o update enrichPeakOverlap to support nShuffle = 0, which now will report only overlay with pvalue = NA <2015-03-29, Sun>
o add facet and free_y parameter for plotAvgProf and plotAvgProf2 <2015-03-29, Sun>
o update docs <2015-03-29, Sun>
o update plotAvgProf and plotAvgProf2 to fully supporting confidence interval,
see https://github.com/GuangchuangYu/ChIPseeker/pull/6 <2015-03-29, Sun>
CHANGES IN VERSION 1.3.12
------------------------
o add confidence interval for plotAvgProf, see https://github.com/GuangchuangYu/ChIPseeker/issues/3 <2015-03-26, Thu>
CHANGES IN VERSION 1.3.11
------------------------
o add citation <2015-03-16, Mon>
CHANGES IN VERSION 1.3.10
------------------------
o update GEO data <2015-03-03, Tue>
CHANGES IN VERSION 1.3.9
------------------------
o add parameter *genomicAnnotationPriority* for annotatePeak function <2015-02-27, Fri>
CHANGES IN VERSION 1.3.8
------------------------
o add DOSE citation <2015-02-13, Fri>
CHANGES IN VERSION 1.3.7
------------------------
o bug fixed in plotDistToTSS <2015-02-06, Fri>
CHANGES IN VERSION 1.3.6
------------------------
o when peak is exactly located at gene end and near the end of chromosome,
NA will be generated and throw error when assigning downstream of gene end.
This bug has been fixed <2015-02-03, Tue>
CHANGES IN VERSION 1.3.5
------------------------
o bug fixed in getNearestFeatureIndicesAndDistances when peak in the
very begining or end of the chromosome <2015-01-30, Fri>
CHANGES IN VERSION 1.3.4
------------------------
o bug fixed for introducing dplyr in plotDistToTSS <2015-01-28, Wed>
CHANGES IN VERSION 1.3.3
------------------------
o update vignette to use BiocStyle::latex() <2015-01-26, Mon>
CHANGES IN VERSION 1.3.2
------------------------
o fixed import issue to meet the changes of AnnotationDbi and S4Vectors <2015-01-22, Thu>
CHANGES IN VERSION 1.1.21
------------------------
o use data.table instead of data.frame to optimize covplot <2014-10-06, Mon>
CHANGES IN VERSION 1.1.20
------------------------
o update annotatePeak to store the seqinfo information <2014-09-30, Tue>
o modified runValue(x) to sapply(x, runValue) <2014-09-30, Tue>
CHANGES IN VERSION 1.1.19
------------------------
o implement csAnno S4 object <2014-09-28, Sun>
o modify plot function for csAnno instance <2014-09-28, Sun>
o implement vennpie function <2014-09-28, Sun>
CHANGES IN VERSION 1.1.17
------------------------
o deprecate plotChrCov to new function covplot <2014-08-18, Mon>
o add new paramter chrs and xlim to covplot <2014-08-18, Mon>
CHANGES IN VERSION 1.1.16
------------------------
o optimize plotChrCov, running time reduce drastically <2014-08-15, Fri>
CHANGES IN VERSION 1.1.15
------------------------
o remove un-mappable peak to prevent fail in peak annotation <2014-08-14, Thu>
CHANGES IN VERSION 1.1.14
------------------------
o bug fixed in plotDistToTSS <2014-08-14, Thu>
CHANGES IN VERSION 1.1.13
------------------------
o change TranscriptDb to TxDb according to GenomicFeatures <2014-07-29, Tue>
CHANGES IN VERSION 1.1.12
------------------------
o bug fixed in plotChrCov <2014-07-21, Mon>
CHANGES IN VERSION 1.1.10
------------------------
o bug fixed in calculating distances from peak end <2014-06-18, Wed>
CHANGES IN VERSION 1.1.9
------------------------
o add level parameter to annotatePeak, and set it to "transcript" by default.
Now annotatePeak will annotate peaks in transcript level
except user specify level = "gene" <2014-06-16, Mon>
o add addFlankGeneInfo parameter to annotatePeak.
If it set to true, all features within the flankDistance will be annotated. <2014-06-16, Mon>
CHANGES IN VERSION 1.1.8
------------------------
o bug fixed when peak overlap with feature <2014-06-11, Wed>
o optimize for getting overlap features of peaks <2014-06-11, Wed>
o update plotAnnoPie, separate the pie and legend to prevent label overlap <2014-06-12, Thu>
CHANGES IN VERSION 1.1.7
------------------------
o bug fixed in calculating distanceToTSS <2014-06-03, Tue>
CHANGES IN VERSION 1.1.6
------------------------
o add chainFile parameter in enrichAnnoOverlap and enrichPeakOverlap to support different genome version comparision <2014-06-01, Sun>
o fixed color bug in peakHeatmap.internal2 and plotAnnoBar <2014-06-02, Mon>
o update vignettes <2014-06-02, Mon>
CHANGES IN VERSION 1.1.5
------------------------
o export getPromoters and getTagMatrix <2014-05-31, Sat>
o rename plotAvgProf to plotAvgProf2 and implement plotAvgProf based on tagMatrix <2014-05-31, Sat>
o implement tagHeatmap for visualize heatmap of the tagMatrix or a list of tagMatrix <2014-05-31, Sat>
o implement shuffle function to generate a random ChIP data based on a real one <2014-05-31, Sat>
o implement enrichPeakOverlap to calcuate significant of ChIP experiments based on the genome coordinations <2014-05-31, Sat>
o implement enrichAnnoOverlap to calculate significant of ChIP experiments based on their nearest gene annotation <2014-05-31, Sat>
o incorporate GEO database for mining significant overlap of ChIP data <2014-05-31, Sat>
+ getGEOspecies summarize the collected data by species
+ getGEOgenomeVersion summarize the colleted data by genome version
+ getGEOInfo extract the information by genome version query
+ downloadGEObedFiles download all bed files of a particular genome version
+ downloadGSMbedFiles download the bed files of the input GSM list.
CHANGES IN VERSION 1.1.4
------------------------
o in the annotation column of output of annotatePeak function,
if Exon/Intron, the output change to 'Transcript_Name/GeneID, Exon no. of total_no.' <2014-05-14, Wed>
CHANGES IN VERSION 1.1.3
------------------------
o bug fixed when metadata(TranscriptDb) contained NA <2014-04-30, Wed>
o support ID type of Ensembl in annotatePeak (Entrez was supported) <2014-04-30, Wed>
CHANGES IN VERSION 1.1.2
------------------------
o implemented plotChrCov <2014-04-25, Fri>
o implemented plotAvgProf and peakHeatmap <2014-04-24, Thu>
CHANGES IN VERSION 1.1.1
------------------------
o output of annotatePeak now contain chromosome length information <2014-04-22, Tue>
o re-implement plotAnnoPie to use ordinary pie plot instead of pie3D <2014-04-21, Mon>
CHANGES IN VERSION 1.0.0
------------------------
o initial version with the following functions implemented:
+ annotatePeak
+ overlap
+ plotAnnoBar
+ plotAnnoPie
+ plotDistToTSS
+ readPeakFile
+ vennplot
+ vennplot.peakfile