NEWS
ChIPseeker 1.49.3
annotatePeak() keeps annotation, geneChr/geneStart/geneEnd, geneId and
transcriptId consistent with each other at transcript level (issue #252). The
transcript id of an exon/intron/UTR hit was taken from
names(genomicRegion)[subjectIndex], indexing the unlisted ranges with the
names of the GRangesList; this mostly returned NA and occasionally a wrong
transcript, so a peak could be reported with the metadata of an unrelated
transcript (even on another chromosome). The ids are now expanded before
indexing, and the Promoter branch writes the feature id reset into anno
instead of a stale local variable, so promoter peaks keep the nearest-TSS
transcript. The same alignment is now applied at level = "gene": the gene of
the overlapping exon/intron/UTR is resolved with TXID2EG() and used instead
of the nearest gene, so geneId/geneStart/geneEnd/distanceToTSS follow
the annotation there as well. (2026-10-01, Thu)seq2gene() no longer fails with $ operator is invalid for atomic vectors
when none of the queried regions overlaps an exon
(getGenomicAnnotation.internal() returns NA then); host-gene extraction is
skipped and the nearest/flanking genes are still reported (issue #248).
(2026-10-01, Thu)getTagMatrix()/plotPeakProf2() no longer fail with
Error in cursor:(cursor + seq - 1) : result would be too long a vector when
type = "body" is used with a flank extension shorter than 1kb (issue #250).
The share of bins of a flank is derived from its actual length (500bp now
contributes 5% of the bins instead of being rounded down to zero), a
non-empty flank always gets at least one column, and the binning loops were
replaced by edge-based averaging of equal-width bins. This changes numbers
slightly: the old code divided the last bin of a section by count-1
instead of count (about 10% too high for a 10 bp bin), and it put all
leftover positions of a section into its last bin instead of spreading them,
which can move that bin considerably (up to ~40% for a 7 bp remainder in a
300 bp bin). The x-axis breaks of plotPeakProf2() are derived from the same
column layout. (2026-10-01, Thu)downloadGEObedFiles()/downloadGSMbedFiles() rewrite the ftp:// urls of
gsminfo$supplementary_file to https:// before downloading and report the
underlying download error when a file cannot be fetched (issue #254).
(2026-10-01, Thu)- An empty input is now handled:
annotatePeak(GRanges(), ...) returns an
empty csAnno instead of failing with "Error: invalid subscript" or
"replacement has 1 row, data has 0". The root cause (follow()/precede()
returning a SortedByQueryHits object instead of indices for an empty query) is
guarded in getNearestFeatureIndicesAndDistances(), which also makes
seq2gene() return character(0) for an empty input. (2026-10-01, Thu)
- Documented the distance definition of
flank_gene_distances reported by
annotatePeak(..., addFlankGeneInfo = TRUE): a distance of 0 means that the
peak overlaps the feature range - at level = "transcript" the feature is the
whole transcript, which is why most entries can be 0 - while non-overlapping
peaks get the signed distance to the feature TSS (issue #235).
(2026-10-01, Thu)
annotatePeak() no longer fails with Error: invalid subscript when every
peak is dropped, which typically happens because none of the seqlevels of the
peaks matches TxDb (chr1 vs NC_000001.11). getGenomicAnnotation() no
longer hands the SortedByQueryHits object returned by follow() for an empty
query to features[], and annotatePeak() now reports the seqlevels
mismatch together with how to align the chromosome names
(seqlevelsStyle()). (2026-10-01, Thu)plotAvgProf()/plotMultiProf() now state which xlim matches the tag matrix
instead of stopping with "please specify appropreate xcoordinations...".
xlim defines the x-axis coordinates, so its width has to match the number of
columns of the tag matrix; the typo is gone and both valid forms
(c(1, nc) and, for a matrix with one column per bp, c(-(nc-1)/2, (nc-1)/2))
are shown (issue #240). (2026-10-01, Thu)enrichPeakOverlap() accepts a single GRanges as targetPeak again: it was
passed on unwrapped while the permutation test works on a list of target peak
sets, so the call failed with "GRanges objects don't support [[, as.list(),
lapply()". The documentation of enrichPeakOverlap()/enrichAnnoOverlap()
now also states the direction of the test - the observed ratio is the fraction
of target peaks covered by the query peaks and the target is the shuffled set
- which explains why
N_OL is identical in both directions while the p-value
is not, and that N_OL of enrichAnnoOverlap() counts genes and can exceed
the number of input peaks (issue #84). (2026-10-01, Thu)
enrichPeakOverlap() gained an opt-in symmetric argument. With
symmetric = TRUE the mirrored direction (query and target exchanged) is
computed as well and the two one-sided permutation p-values are combined as
min(1, 2*min(p, p_rev)) (Hedges), so the result no longer depends on the
order of the arguments. The default stays FALSE (one-sided) and all existing
numbers are unchanged; the mirrored test doubles the number of permutations and
raises the smallest reportable p-value to 2/(nShuffle+1). enrichAnnoOverlap()
needs no such argument, its hypergeometric p-value is already exactly symmetric
(issue #84). (2026-10-01, Thu)upsetplot(vennpie = TRUE) can be drawn again with ggplot2 >= 4.0. The vennpie
sub-view is embedded as an annotation_custom() layer, which ggplot2 only
supports below coord_cartesian(), so the sub-view no longer uses
coord_fixed(). No replacement for it is added: ggplotify rasterises the grob
with the aspect ratio of the device, and forcing a square panel distorted the
venn diagram further (measured anisotropy 1.43 without versus 1.50 with
theme(aspect.ratio = 1), against 1.41 for the undistorted drawing). Before, the
plot failed with `annotation_custom()` only works with `coord_cartesian()`.
Note that ggupset 0.4.1 itself still maps the deprecated size aesthetic, so
drawing the plot may print "Please use linewidth instead"; the warning comes
from ggupset (https://github.com/const-ae/ggupset/issues) and can be ignored.
(2026-10-01, Thu)
ChIPseeker 1.49.2
annotatePeak() now reports geneChr and geneStrand as characters instead of
factor codes. as.data.frame() returns 'seqnames'/'strand' as factors and
assigning a factor into mcols() dropped the class, so both columns came out
as integers (e.g. geneStrand = 1/2 instead of +/-, and a wrong geneChr
whenever the seqlevels were not in numeric order) (issues #233, #247).
(2026-09-15, Tue)annotatePeak() now warns when peaks are dropped because no feature of TxDb
can be found for them (e.g. peaks on contigs/scaffolds without genes, or a
seqlevels style mismatch). Previously they disappeared silently (issues
#251, #258). (2026-09-15, Tue)annotatePeak(..., sameStrand = TRUE) no longer assigns a peak to a feature on
the opposite strand. Overlap detection in getNearestFeatureIndicesAndDistances()
was calling findOverlaps() with unstrand(features), which bypassed sameStrand
and overrode the strand-aware nearest-feature result (issues #257, #258). Peaks
with ambiguous strand (*) are unaffected and still match features on any strand.
(2026-09-14, Mon)plotAnnoBar() no longer uses the deprecated ggplot2::aes_string() (issue #268).
It follows the tidy evaluation idiom already used by plotDistToTSS().
(2026-09-14, Mon)upsetplot() no longer uses the deprecated ggplot2::aes_(); the x aesthetic is
now mapped with .data$anno, the same tidy evaluation idiom used by
plotDistToTSS(). (2026-09-17, Thu)- dropped unused
@importFrom directives that have no call site in the package
(ggplot2::geom_text, ggplot2::geom_segment, ggplot2::scale_fill_brewer,
ggplot2::scale_fill_hue), so the generated NAMESPACE imports less.
(2026-09-17, Thu)
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
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
ChIPseeker 1.19.1
- add
origin_label = "TSS" parameter to plotAvgProf (2018-12-12, Wed)
ChIPseeker 1.18.0
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)
ChIPseeker 1.16.0
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>
- change
plotAvgProf's default y label <2018-03-14, Wed>
- plotAnnoBar now visualize barplot according to the order of input list
(y-axis) (2018-02-27, Tue)
- follow renaming of RangesList class -> IntegerRangesList in IRanges v2.13.12
ChIPseeker 1.15.3
- options to ignore '1st exon', '1st intron', 'downstream' and promoter
subcategory when summarizing result and visualization (2018-01-09, Tue)
- throw msg of 'file not found and skip' when requested url is not available
when downloading BED file from GEO (2017-12-28, Thu)
- bug fixed of getGene (2017-12-27, Wed)