update test
 

 update websites
 

 update man
 

 Merge branch 'master' into devel
 

 trim line length
 

 update man
 

 change 1:... to seq_len()
 

 update biocViews
 

 fix too long line
 

 rm docs
 

 mention other vignettes in introduction
 

 add scripts inst/scripts/graph_example.R
 

 rename vignettes-table
 

 rename: vignettes/PoemOnSpatialExperiment.Rmd
 

 Merge branch 'master' into devel
 

 fix git repo issue
 

 cp data generation scripts to inst/scripts/
 

 change description
 

 replaced sapply with vapply
 

 some small bioc coding style changes
 

 added matchSets test
 

 added unit tests
 

 changed default metric to something that works with negatives
 

 README: update bioconductor installation
 

 replaced sapply with vapply
 

 some small bioc coding style changes
 

 added matchSets test
 

 added unit tests
 

 changed default metric to something that works with negatives
 

 removed Rhistory
 

 added some text
 

 Updated documentation
 

 Updated region plot x and y axis labels
 

 Changed documentation hard wrapping
 

 Remove accidental line
 

 bump ver
 

 require c++14
 

 version bump
 

 add BiocStyle to suggest
 

 bug fix
 

 version bump 2.19.9
 

 report message from content in .invoke_fun
 

 version bump 2.19.8
 

 add test-coverage.yml
 

 SparseArray 1.7.3

A couple of minor edits to the vignette.
 

 UCSC.utils 1.3.1

Minor edit to vignette.
 

 version bump 1.19.5
 

 minor edit to Service call in Dockstore
 

 add host slot to Service object
 

 bug fix
 

 trigger rebuild
 

 version bump in devel
 

 HDF5Array 1.35.4

Minor edits to "HDF5Array performance" vignette.
 

 0.99.8 tweak for bioconductor build testing
 

 Merge pull request #6 from davemcg/devel

Small tweaks 

 Merge pull request #4 from davemcg/devel

0.99.4  

 update news, description 

 fixes bug in kway-merge that would cause crashes; adds additional logging
 

 Fixes bug with inplace mergesort, convert unsafe alloc to safe alloc
 

 fixes minor bug causing overflow in nodes that don't have edges
 

 Merge pull request #61 from ahl27/master

feat: Speed enhancements for `ExoLabel` 

 Minor man page updates
 

 Formatting updates and more comments
 

 remove old name :(
 

 more slight adjustments to edge compression strategy
 

 fix small bug
 

 adds option to switch between in-place or regular mergesort for performance
 

 Merge branch 'npcooley:devel' into master
 

 minor edits for clarity
 

 DOESNT WORK DO NOT MERGE -- saving progress on implementation, still need to fix open issue with reading in edges
 

 Adds first iteration of losertrees, still contains some debugging functions
 

 v1.41.1 -- attempt to fix issue with edgeR citations
 

 v1.3.1 update
 

 1.15.102  `plot_coef_densities` : coef <- density <- NULL
 

 1.15.100  `plot_survival` : outcomment pdf printing (prevent file access issues)
 

 1.15.98  `process_maxquant` :  reverse <- NULL
 

 1.15.96  rm_diann_contaminants : drop @param contaminants
 

 1.15.94  Improve/Unify contaminant handling
 

 1.15.92  Hardcode `statvars` in fitters
 

 1.15.90  `plot_coef_densities` fixes (check)
 

 1.15.88 DESCRIPTION: mv `survival` from Suggests to Imports
 

 1.15.86  `add_adjusted_pvalues` : return object unaltered when pvalues lacking (pca)
 

 1.15.84  `add_facetvars` : effectvalues replaced by tvalues
 

 1.15.82  .extract_sign_features : now t-based (rather than effect-based)
 

 1.15.80  biplot_dims : effect-based -> t-based
 

 1.15.78  effect~.~pca -> t~.~pca
 

 1.15.76  analyze: fit > fit_linmod
 

 1.15.74  DIMRED -> DIMREDENGINES
 

 1.15.72  Rm `survminer` from Suggests
 

 1.15.70  Rm `dichotomize_exprs` and `.dichotomize_exprs` (fit_survival now reimplemented differently)
 

 1.15.68  Rm `.plot_survminer` and `plot_survminer` (now replaced by plot_survival)
 

 1.15.66  rm `download_tcga_example` (nrow replaced by survival_example)
 

 1.15.65  Rename `fit` into `fit_linmod`
 

 1.15.63  survival: improve example, rm unnecessary filter
 

 1.15.62  survival: simulation example and `conf.int` argument
 

 1.15.61 survival: switch from `2-` notation to `<2`
 

 1.15.59  fit_survival: summarize_fit
 

 1.15.57  plot_survival: improve messaging
 

 1.15.56  `plot_survival`: allow `percentile` to be a vector
 

 1.15.54  `fit_survival` : compute (p|effect|t) for both logrank and cph
 

 1.15.52  fit_survival : writefun -> writefunname
 

 1.15.50  `(fit|plot)_survival` : mv documentation to fit_survival (rather than plot)
 

 1.15.48  `plot_coef_densities` (experimental)
 

 1.15.46  plot_volcano : selected features should always be printed
 

 1.15.44  read_diann : fill empty protein values with uniprot (and not opposite)
 

 1.15.42  `plot_exprs`: softcode `features` to plot no matter what
 

 1.15.40  Change linmod defaults : contrast_coefs -> model_coefs
 

 1.15.38  plot_exprs : xlab = NULL -> x (continuous variables ! )
 

 Version Bump
 

 Fixed Badge Links
 

 Formatting in README
 

 Multiple minor updates

- better GitHub README
- updated DESCRIPTION to latest Roxygen
- removed MNAR dataset function, this should be in an experiment -  not in the package
 

 HDF5Array 1.35.3

Add "HDF5Array performance" vignette.
 

 Fix having a only single variate
 

 Version bump
 

 Version bump
 

 Use machine epsilon instead of exact match for test
- replaceNAs with row mean was producing slightly different results
 

 Update README
 

 Remove deprecated zlibbioc dependency
 

 Bioc version bump 0.99.12
 

 bump
 

 Fix typo
 

 Update vignette to replace data upload from azure to temporary location
 

 Fix adjacency tests
 

 C++11
 

 Merge remote-tracking branch 'bioc/devel' into HEAD
 

 back to original r and bioc versions
 

 remove dist from tune.pls - typo
 

 Merge pull request #349 from mixOmicsTeam/303-perf-multiple-solutions

update perf to deal with multiple replacement plus prints warning 

 Merge pull request #348 from mixOmicsTeam/issue-304-streamline-tune

Issue 304 streamline tune 

 revert back vignette change
 

 install mixomics from github inside the vignette
 

 update tune.plsda to work on multilevel and add example
 

 add multilevel examples to tune.pls and tune.spls
 

 fix unit tests checking plotting properly
 

 shortern example lines
 

 add unit tests for tune.block.plsda
 

 unit tests for tune.pls
 

 add examples to perf.assess
 

 update output docs for perf
 

 add unit tests for tune.pca and match default args
 

 how to use 'measure' arg in tune mint functions
 

 clean tune tune.plsda and tune.splsda input args
 

 fix notes in docs
 

 fix notes and warnings in tune docs
 

 fix warnings in tune.pls
 

 fixed docs warnings
 

 fix errors in tune.spls docs
 

 make tune.spls example code lines less long
 

 streamline tune.plsda - no 'measure' arg
 

 update tune.block.splsda docs to reflect how to use 'dist' and 'measure'
 

 clean up input params docs
 

 update unit test for removing plot from tune.rcc
 

 start streamlining tune wrapper function
 

 update examples of tune.mint.plsda
 

 init tune.mint.plsda
 

 add unit tests for tune.mint.splsda
 

 update tune.mint.splsda docs and example
 

 init tune.block.plsda
 

 typos in tune.block.splsda
 

 add tune.pls examples
 

 update tune.spls docs
 

 add tune.spls examples to docs
 

 add unit test for new tune.spls functionality
 

 add tune.plsda examples
 

 update tune.splsda docs
 

 add unit testing for edited tune.splsda functionality
 

 update github repo readme with updates from oct and nov
 

 version bump 6.30.4
 

 perf.assess.mint output should be perf - hangover from perf PR
 

 change output format for perf.assess.sgccda
 

 change perf.assess object so cant be plotted
 

 Update bug_report.md remove al assignee 

 update perf assess mint unit tests
 

 streamline perf.assess.mint.plsda to only output ncomp
 

 update documentation to reflect changes in perf.assess so far
 

 unit testing for perf and perf.assess diablo
 

 init perf.assess.diablo
 

 finalise perf.assess function
 

 debugging perf.assess
 

 typo
 

 init perf.assess.pls and perf.assess.spls functions
 

 rename function and remove warning for choosing ncomp and perf.assess does not choose ncomp
 

 unit testing to check result of perf.assess.plsda in serial and parallel compared to perf for same ncomp
 

 add test for perf.assess.plsda
 

 Merge pull request #342 from mixOmicsTeam/fix-github-actions-linux

Fix GitHub actions linux 

 comment out linux install extra dependencies
 

 remove coordinate check due to OS differences
 

 adjust test to reflect possible sign change during plotting
 

 update tests without scheme arg
 

 hardcode scheme and init for wrapper gcca functions
 

 update mint block functions to hardcode init and scheme
 

 fix tests which specify a scheme when running block.splsda
 

 add note in docs that functions have hardcoded scheme and init
 

 Update README.md github install correct command 

 update block.plsda to hardcode scheme and init
 

 update docs
 

 Merge pull request #338 from mixOmicsTeam/issue-334

Issue 334 

 check all params documented in tune wrapper
 

 add seed arg to tune.block.splsda
 

 add seed arg to tune.splslevel
 

 add seed to tune.spls and tune.spls1
 

 Merge pull request #337 from mixOmicsTeam/335-feature-request-pass-seed-argument-to-perf-functions-for-better-reproducibility

335 feature request pass seed argument to perf functions for better reproducibility 

 force github action to use bioc version 3.20
 

 debug bioc latest version error
 

 force github action to use release r version
 

 speed up tests to meet github action 6 hours limit for code coverage
 

 update perf docs and examples to reflect BPPARAM and seed args
 

 set seed arg in perf.diablo and unit test
 

 add seed argument for reproducible perf.splsda
 

 confirm perf gives same result with seed in series and parallel
 

 modify tests to reflect slight changes now BPPARAM is set
 

 Merge pull request #333 from mixOmicsTeam/issue-216

Issue 216 - BPPARAM in `tune` and `perf` functions 

 speed up tune testing
 

 hide warning messages
 

 add tune.bloc.splsda to tune wrapper and unit test, passes checks locally
 

 typos in tests
 

 update perf.mixo_plsda and perf.mixo_splsda testing
 

 load biocparallel before running tests
 

 update perf doc
 

 update perf doc
 

 fixed testing errors to do with speed comparisons in serial and parallel
 

 change from cpu to BPPARAM in perf examples
 

 pass BPPARAM param through tune.spls to tune.spls1
 

 update perf documentation
 

 load biocparallel library for testing
 

 test that tune.spca works indepdently and in tune wrapper
 

 add more tests for tune.space
 

 updated test for tune.splsda to reflect changes
 

 updated tune.splda and internal function MCVfold.spls so uses 'BPPARAM' instead of 'cpu' and 'parallel' args to run in parallel
 

 fix typo in summary documentation
 

 fix bookdown link
 

 added extra tests to deal with all plotting styles
 

 add more detailed tests
 

 add tests for plotIndiv checking input arguments
 

 Merge pull request #325 from mixOmicsTeam/update-readme

Update readme 

 add version badge
 

 rename r cmd check action to try to fix badge
 

 change back
 

 try event pull request on build check badge
 

 update codecov badge
 

 update rcmdcheck badge
 

 updating badges in readme
 

 version push 6.29.3
 

 remove test coverage and slack notify from actions
 

 try usethis to set up new
 

 fix: in plotIndiv function the order of pch levels are now correct in legend
 

 Version bump
 

     Accommodate changes from DropletUtils::emptyDrops()

- Knock-on effect of changes to `tenx-unfiltered-pbmc4k.Rmd` in **OSCA.workflows** (https://github.com/OSCA-source/OSCA.workflows/commit/6ab1fc45a33848136d6ac0282c42b0ece5e2476a)
- Details of changes: MarioniLab/DropletUtils#118
- Results in slightly different set of non-empty droplets which causes knock-on changes to the cluster label
 

 Accommodate changes from DropletUtils::emptyDrops()

- Knock-on effect of changes to `tenx-unfiltered-pbmc4k.Rmd` in **OSCA.workflows** (https://github.com/OSCA-source/OSCA.workflows/commit/6ab1fc45a33848136d6ac0282c42b0ece5e2476a)
- Details of changes: MarioniLab/DropletUtils#118
- Results in slightly different set of non-empty droplets which causes knock-on changes to the cluster labels
 

 Tweak GO terms used

- GO:0019432 now has highest average and median expression in cluster 4 (just barely), which breaks the sanity check
- Easiest just to switch up the text to focus on a different GO term
- Similar to change made in 8be03135f074bd5872c48a047fff654a033720fd (BioC 3.20)
 

 Add summary for regROTS objects
 

 Export pdf with visible layers only
 

 Switch off using UCSC RepeatMasker annotations when they are not available, fixing also intergenic alignment fraction estimation. Fix documentation links.
 

 Seq info matching during diagnostic happens only when species metadata is available
 

 Add plotting of regROTS objects
 

 depends on R >= 4.5
 

 address 'R CMD check' warnings
 

 Fix situation with non-working models
 

 Update NEWS
 

 update seqVCF2GDS()
 

 Updated fix for removal of zlibbioc
 

 version bump 1.17.3
 

 Add missing dependencies in the DESCRIPTION file
 

 Add missing row_number
 

 Version bump
 

 bump version
 

 Updated NEWS
 

 fix: solved  bug and adapted unit tests
 

 Merge branch 'master' of https://github.com/rformassspectrometry/QFeatures into issue206
 

 Version bump
 

 fixed a bug of finding nearest exon
 

 Accommodate changes from `DropletUtils::emptyDrops()`

- Details of changes: https://github.com/MarioniLab/DropletUtils/issues/118
- Results in slightly different set of non-empty droplets, which causes knock-on changes to the cluster labels
 

 updated news with fix of the tooltip behavior
 

 fixing the behavior of the tooltip title, thanks to the suggestion provided by @thomas-keller!
Fixes the https://github.com/federicomarini/GeneTonic/issues/61
 

 Merge pull request #12 from Egors01/merge_bc

Merge bioc release 

 late version bump
 

 Merge pull request #11 from Egors01/add_abundance

added raw counts to pvalue calculation 

 revert