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Changelog

Source: NEWS.md

igvShiny 1.9.42

  • Switch the hg19 and hg38 assets to igv.org, off a hgdownload host answering in tens of seconds (#167)
  • Use the tabix-indexed RefSeq annotation, so startup reads the locus rather than the whole genome (#167)
  • Fix the demo BAM track, which drew GRCh37 reads against the hg38 reference (#168)

igvShiny 1.9.41

  • Split the demo apps so each covers one feature in under sixty lines, adding gff3.R and junctions.R (#64)
  • Move the showcase app to inst/showcase, leaving inst/demos for the focused examples (#64)
  • Drop the makefile targets naming demo files removed in #156

igvShiny 1.9.40

  • Switch the custom genome example to the sarsGenome files the package ships, keeping R CMD check offline
  • Wrap the remote GWAS example in donttest, since the GWASTrack constructor checks that the url resolves

igvShiny 1.9.39

  • Prevent the getting-started vignette from reaching gladki.pl while the package builds (#158)

igvShiny 1.9.38

  • Add loadSpliceJunctionTrackFromLocalData, writing junctions held in R as the bed igv.js reads (#103)
  • Support merged tracks in the startup track list, drawing junction arcs over a coverage track (#103)
  • Extend the track option allowlist with alpha, the blend a merged track hands its members (#103)

igvShiny 1.9.37

  • Add the Track options reference vignette, covering every track type and its options
  • Replace the overview vignette, whose content the two remaining vignettes already held
  • Move the http custom genome example into the getting started vignette

igvShiny 1.9.36

  • Remove 14 track options igv.js never reads, which reached the browser and were ignored (#159)
  • Add negColorScale and posColorScale, the gradients seg tracks read (#159)
  • Add a test holding the option allowlist to the bundled igv.js build (#159)

igvShiny 1.9.35

  • Rewrite the demo apps on bslib, replacing 15 legacy apps with 7 single-topic ones (#64)
  • Remove the forked Connect app, which now runs the package demo itself (#64)
  • Extend the flagship demo with the splice junction and removeTracksByName calls (#64)

igvShiny 1.9.34

  • Rename the tair10 gene track to the registry name, breaking removeTracksByName on the old label (#143)

igvShiny 1.9.33

  • Fix the off-by-one start in currentGenomicRegion, closing its round trip through showGenomicRegion (#126)

igvShiny 1.9.32

  • Add loadSpliceJunctionTrackFromURL, drawing STAR splice junctions from a bed file (#103)
  • Extend the track option allowlist with the igv.js splice junction filters and labels (#103)
  • Fix the dead asset URLs in the bundled igv.js examples, and scan that directory (#103)

igvShiny 1.9.31

  • Add loadCramTrackFromLocalData, serving a cram file and its index to igv.js (#102)
  • Extend the loader tests with the local cram payload and the staged files

igvShiny 1.9.30

  • Allow alignment tracks to sort their reads by a bam tag through trackConfig (#104)
  • Add a test pinning the sort object sent to igv.js

igvShiny 1.9.29

  • Resolve tair10 through the igv.js registry, dropping the self-hosted fasta (#143)
  • Read the rhos sequence and genes from the UCSC assembly hub instead of gladki.pl (#143)
  • Remove the hg19 Gencode v18 track, whose s3 bucket answers 403 (#143)

igvShiny 1.9.28

  • Fix a second igvShiny widget staying silent at a locus another one already reports (#126)
  • Add a headless test moving two widgets on one page to the same region

igvShiny 1.9.27

  • Remove the mm10 and danRer11 reference workaround, unneeded with igv.js 3.x (#107)
  • Drop four unused igv.js builds and the unreferenced stylesheet from the package
  • Read the genome registry igv.js 3.x uses and document the UCSC dependency it carries

igvShiny 1.9.26

  • Update the Connect Cloud manifest, which pinned a commit older than the demo
  • Expose the installed igvShiny version in the demo sidebar

igvShiny 1.9.25

  • Allow a gwas column mapping through trackConfig, for loadGwasTrack callers
  • Extend the Connect Cloud demo with a gwas track using custom columns and colors

igvShiny 1.9.24

  • Send the gwas column mapping to igv.js, so any data frame layout works (#32)
  • Support a chromosomeColorMap argument coloring gwas points per chromosome (#46)
  • Prevent out-of-range gwas column numbers from yielding a silently empty track

igvShiny 1.9.23

  • Restore the full three-system matrix on every pull request
  • Remove the full-ci label, redundant once macOS and Windows finish in minutes
  • Correct the macOS libxml2 config path, wrong since the runners moved to arm64

igvShiny 1.9.22

  • Reduce the pull request matrix to Linux, running macOS and Windows on master and nightly
  • Enable a full-ci label to force the whole matrix on a pull request

igvShiny 1.9.21

  • Bump the GitHub Actions used in CI to their current major versions
  • Replace the mutable upload-artifact@master reference with a released version

igvShiny 1.9.20

igvShiny 1.9.19

  • Reduce bioconductor.org round trips in CI and cancel superseded pull request runs
  • Disable the BiocCheck deprecation lookup, the last CI step reaching bioconductor.org
  • Prevent the macOS and Windows jobs from rebuilding every package on each run

igvShiny 1.9.17

  • Enforce green CI on macOS and Windows by dropping the allow-failure matrix flags

igvShiny 1.9.16

  • Add a getting-started vignette covering the widget, track loaders, navigation and modules

igvShiny 1.9.15

  • Fix the 404 on locally written tracks when the tracks directory moves

igvShiny 1.9.14

  • Allow igvShiny() to build outside a shiny session, for scripts and vignettes

igvShiny 1.9.13

  • Prevent NA or empty names in trackConfig, warning instead of erroring
  • Enforce a non-empty scalar string for the startup track url

igvShiny 1.9.12

  • Add unit tests for the track loaders, driven by a fake Shiny session (M3)
  • Replace the gladki.pl test fixtures with a local httpuv static server
  • Extend test coverage from 16% to 92% (M3)

igvShiny 1.9.11

  • Enable the covr coverage step on every Linux CI build (M3)
  • Add covr to Suggests

igvShiny 1.9.10

  • Wrap the 25 over-long lines in R/igvShiny.R at 80 characters (BiocCheck)
  • Move paste() out of warning() calls, keeping the message text unchanged
  • Exclude local *.BiocCheck/ output folders from git

igvShiny 1.9.9

  • Bump the bundled igv.js from 2.13.1 to 3.8.4 (minified) and update the locuschange handler for the 3.x event payload — it now reads the locus from the referenceFrameList and keeps the whole-genome “all” view working (#116)

igvShiny 1.9.8

  • Add labels to all vignette code chunks (BiocCheck)
  • Add the R Consortium fnd (funder) role to Authors@R — the ISC grant funding this work (BiocCheck)

igvShiny 1.9.7

  • Add a public, clickable demo app deployed on Posit Connect Cloud, plus the repository’s first README (#117, #118)
  • Add a modern bslib (Bootstrap 5) UI to the Connect demo — grouped controls, themed layout, IGV viewer in a full-screen-able card (#119)

igvShiny 1.9.6

  • docs: credit past contributors in DESCRIPTION — Carolina Heimann, Steffen Klasberg, Vincent Carey, Parv Sachdeva and Mateusz Gladki are now listed as ctb

igvShiny 1.9.5

igvShiny 1.9.4

  • fix: pass autoscaleGroup through in loadBedGraphTrackFromURL (#105, thanks @M4teuszzGl4dki)
  • fix: support string-based autoscaleGroup values in both bedGraph handlers

igvShiny 1.9.3

  • ci: fix Windows/macOS CI failures (install pkgload alongside pkgdown)
  • ci: add automated push to Bioconductor devel on merge to master

igvShiny 1.9.2

  • fix(ci): add testthat to Suggests field in DESCRIPTION to fix warning

igvShiny 1.9.1

  • fix(ci): remove missing test_igvShiny_package.R from Collate field to fix build error

igvShiny 1.9.0

  • Version bump due to Bioconductor 3.23 devel synchronization.

igvShiny 1.5.2 - 2025-09-02

  • support passing additional track options to igv.js

igvShiny 1.5.1 - 2025-09-01

  • migrate from RUnit to testthat

igvShiny 1.1.5 - 2024-08-29

  • fix issue with loading bed files when app is run with query strings

igvShiny 1.1.4 - 2024-08-25

  • switch from Rcurl::url.exists to httr::http_error (Windows compatibility)

igvShiny 1.1.3 - 2024-08-25

  • stop using Amazon S3 URLs by default

igvShiny 1.1.2 - 2024-08-16

  • fix issue with VCF files

igvShiny 1.1.1 - 2024-08-10

  • fix issue with custom files not working properly

igvShiny 1.0.0 - 2024-08-10

  • sync with Bioconductor (3_19 release)

igvShiny 0.99.7 - 2024-04-23

  • change file links from igv-data.systemsbiology.net to gladki.pl/igvr

igvShiny 0.99.6 - 2024-03-16

  • add shinytest2 for igvShinyDemo-GFF3.R

igvShiny 0.99.5 - 2024-03-14

  • fix issues with GFF3 data
    • make igvShiny demo app for GFF3 working
    • update trackName of GFF3 (from URL)
    • udpate path to local GFF3

igvShiny 0.99.4 - 2024-02-28

  • add pkgdown content

igvShiny 0.99.3 - 2024-02-16

  • fix bug in function loadBamTrackFromLocalData
  • improvge way of loading BAM files - show mismatches

igvShiny 0.99.2 - 2024-02-09

  • fix some Bioconductor NOTEs

igvShiny 0.99.1 - 2024-02-05

  • fix some Bioconductor NOTEs

igvShiny 0.99.0 - 2024-02-04

  • make the first Bioconductor release