Revert "stupid change"

This reverts commit 53c230d41fe9cd70a69686098a9f2ebf2f665e9c.
 

 start fixing output report
 

 remove RhpcBLASctl
 

 use `BiocStyle`
 

 Merge branch 'master' of github.com:SydneyBioX/scFeatures
 

 version bump
 

 Problem with show_symbol when rowData only has one column
 

 plotGeometry
 

 Plot cell density bin2D for multiple samples. Also changed defaults from sample_id = NULL to sample_id = "all"
 

 Install Bioc version 3.16 for codecov
 

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 

 Delete pkgdown_dev. Use fork instead
 

 Also add facet_by to plotColDataHistogram. And rename the argument from sfe to sce since these plotting functions are non-spatial.
 

 Added facet_by to plotColDataBin2D, such as to plot different samples in different facets.
 

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 

 New unit test for localResults and multiple samples
 

 Merge branch 'main' of github.com:pachterlab/voyager
 

 Removed aes_string, which is deprecated.
 

 Merge branch 'RELEASE_3_16' of git.bioconductor.org:packages/Voyager
 

 Fixed bug in show_symbol in moranPlot
 

 Version bump for bug fix
 

 Merged from main

Merge branch 'main' into RELEASE_3_16
 

 Added Kayla
 

 Merge remote-tracking branch 'origin/master'

 

 Update README.md 

 upload logo with transparent background 

 Merge remote-tracking branch 'origin/master'

 

 Update README.md 

 Update README.md 

 Update README.md 

 Merge remote-tracking branch 'origin/master'

 

 added hit badge 

 draft CNV and motif functions 

 

 implement hg38 reference genome and user specified reference genome
 

 added option for custom function for IMD cutoff value. And allow user to specifiy search method
 

 rebase
 

 Update of gc
 

 remove large file
 

 add web page
 

 remove ensembldb::select from namespace
 

 new benchmark
 

 move dev functions so that they are loaded
 

 add refactoring code
 

 Version bump in dev branch.
 

 Improved the documentation of data formatting with "general" option.
 

 Updated vignette (the overview jpg)
 

 Updated all vignettes.
 

 Updated citation to current version.
 

 Try adding another vignette
 

 bump version
 

 fix `cnetplot()` for `node_label` parameter is flipped
 

 bug fixed
 

 Merge pull request #39 from YuLab-SMU/master

merge 

 enable `dotplot()` and `autofacet()` for `gseaResultList` object
 

 Update DESCRIPTION 

 Merge pull request #43 from Vitek-Lab/develop

minor bug fixes to code creation 

 Merge from main

Merge branch 'main' into devel
 

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 

 Rownames woes, and do test for rownames in unit tests
 

 Version bump devel branch for bug fix
 

 Correctly move spatialCoords in removeEmptySpace
 

 use flowjo_biexp_trans in scale_x_logicle to avoid DidNotConverge error #88
 

 Merge branch 'master' of git.bioconductor.org:packages/basilisk.utils
 

 Adapt test_Rle_runq_integer() to a change in R-devel's quantile()

The (undocumented) change in the behavior of quantile() has to do with
the class of the returned object when the input is an integer vector:

- In R < 4.3:
   > x <- sample(99, 20)
   > sapply(1:9, function(type) class(quantile(x, type=type)))
   [1] "integer" "numeric" "integer" "integer" "numeric" "numeric" "numeric"
   [8] "numeric" "numeric"

- In R >= 4.3:
   > sapply(1:9, function(type) class(quantile(x, type=type)))
   [1] "numeric" "numeric" "numeric" "numeric" "numeric" "numeric" "numeric"
   [8] "numeric" "numeric"

So in R >= 4.3, the returned class is always numeric, whatever the input or
quantile algorithm specified via the 'type' argument.

This change broke the tests in test_Rle_runq_integer(). This commit adapts
the tests to make them work again with the new behavior of quantile().
 

 add instructions for r2u
 

 Corect version bump to comply Bioc policy
 

 Merge branch 'master' into RELEASE_3_16
 

 version bump
 

 version bump
 

 Minor
 

 changed to version 1.7.1
 

 .C() functions implemented
 

 dynamic managing c files
 

 num mod lower
 

 num samples corr
 

 Matched to Multi
 

 version update
 

 removed log messages
 

 Merge pull request #31 from ahl27/master

fix: bugfixes and features for `ShuffleC` 

 Merge branch 'npcooley:master' into master
 

 Merge pull request #30 from ahl27/master

TreeDistance, RNG, CorrGL, Refactor 

 feat: C Replacement for `sample`, bootstrapping for `GainLoss` (#10)

* added bootstrapping for gainloss method

* adds bootstrap test, adds new shuffle function with R accessor 

 fix: remove old code, adjust random projection length (#8)

minor bugfixes 

 feat: RNG, Random Projection for MirrorTree (#6)

* adds `TreeDistance` predictor for ProtWeaver, various other optimzations and bugfixes

* fixing rcmdcheck/BiocCheck warnings

* fixing some internal RNG stuff, updates news and description

* removes test function

* fixing rcmdcheck errors 

 version update
 

 fixed missing import
 

 Rename check to check.yaml 

 testthat
 

 removed warning from kable in the loop
 

 examples
 

 Merge commit '5804d63a18e68c21a9e1ca00d09b1992dd268be5'
 

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 

 Merge remote-tracking branch 'upstream/master'
 

 fixed two clustering bugs
 

 DESCRIPTION
 

 better charts with kableExtra
 

 Merge remote-tracking branch 'upstream/master'
 

 GHA update
 

 Fixed errors in SVG feature extraction and detect_cluster.R, which arose in Bioc Devel.
 

 Fixed a bug in col_bar.R
 

 Merge branch 'RELEASE_3_16' into master 

 update github installation documentation

 

 update RELEASE version number
 

 bug fix: update citation
 

 update RELEASE version number
 

 update version number
 

 update version number
 

 update version number
 

 NEWS updated
 

 Minor change: show explicitly that genome is an option in loadVCFs()
 

 bug fixes and updates: kinaseSubstrateScore utilises different species
 

 add filepath option
 

 Merging commits
 

 import functions
 

 import package
 

 Added plotting parameters in kinaseSubstrateHeatmap function
 

 Update DESCRIPTION 

 Merge pull request #41 from Vitek-Lab/develop

minor bug fixes 

 minor bug fixes
 

 Update DESCRIPTION 

 Merge branch 'master' of github.com:mixOmicsTeam/mixOmics
 

 Fix for Issue #270 (#271)

fix: changed the depreciated `size` parameter to `linewidth` and changed `aes_string()` to `aes()`

fix: additional `aes_string()` call changed to `aes()`

fix: changing `aes_string()` to `aes()` introduced error. Adjusted `geom_path` calls so X and Y vectors are appropriately set

refactor: removed some commented lines

tests: added test for `plotIndiv.mint.plsda()` with `ellipse = TRUE` 

 fix FCONE
 

 Deprecation

 - unresponsive
 

 update configure.ac to use C++

- test for sys/mman.h
- use AC_SEARCH_LIBS() to add -lrt if necessary, instead of
  AC_CHECK_LIB(), as recommended by
  https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Libraries.html
- updates #93, updates #94
 

 version bump and NEWS entry
 

 Fix issue 234

- Recover the replaced variables in the global environment after the worker finishes its job
 

 use IS_BIOC_BUILD_MACHINE instead of BBS_HOME
 

 Habil: Version 1.23.4
 

 Add Matrix dependency
 

 update news entries for earlier versions
 

 update NEWS
 

 ignore build_site products and caches
 

 version bump
 

 option for uploading sorted taxon list
 

 adding package guide v3.0
 

 [U] Update to 1.9.1
 

 [FIX] Fixed code for tidyselect warnings, minor adjustments
 

 Remove HTML from web service's reply. (#15)

 

 Merge branch 'remove_R_front'
 

 edgeR 3.41.2
- Update NAMESPACE for getNormLibSizes()
- Add getNormLibSizes() to calcNormFactors example.
 

 BN_mod_res update
 

 omics_to_list add
 

 edge_types simplified
 

 package:: removed
 

 citation
 

 DESCRIPTION modified
 

 MatchedAssayExperiment hidden functions
 

 problems with vignette build
 

 fix URL for clans
 

 fix warning in bioconductor build (edgeR)
 

 v1.11.2 -- tentative change
 

 Register some additional NCBI assemblies

- Assemblies bCatUst1.alt.v2 and bCatUst1.pri.v2 for Catharus ustulatus.
- Assemblies felCat9.1_X and F.catus_Fca126_mat1.0 for Felis catus.
 

 add pointers to data checks
 

 Update news.
 

 Merge remote-tracking branch 'upstream/master'
 

 Merge pull request #5 from mzytnicki/selfInteractionRatio

Change the computation of selfInteraction (diagonal only) + review the distance normalisation 

 pass tests
 

 recompile example data
 

 add missing argument
 

 correct computation of selfInteractionRatios
 

 factorize the creation of the interactionSet in parsers, recreate the interacion on diagonal if there is only off diagonal interaction
 

 rechange compartments affectation, correct tests, recompile example data
 

 allow results of only one condition
 

 change compartment assignment (higher = A). Recompile example data, change tests.
 

 correct tests according to changes on norm distance, ratios and new colors on plotInteractions
 

 Version bump.
 

 allow a transformX parameter in plotDistanceEffect, 3 colours fo plotInteractions
 

 normalization distance : put again results in original scale. Too hard to viz interactions and distance effect otherwise
 

 correct variance for variance by column (by replicate, condition)
 

 rename compartment -> cluster when its cluster and not compartment
 

 log2 normalization for norm distance, keep in log2 after
 

 use log to normalize distance (loess done on log). Dividing by resulting value (equivalent to remove bias in log scale)
 

 add hicpro validPairs
 

 GHA update
 

 GHA update
 

 Merge pull request #31 from rformassspectrometry/jomain

refactor: use grr::matches do match data to samples 

 Update NEWS.md

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

 refactor: use grr::matches do match data to samples

- Use the `grr::matches` function instead of an `lapply` to find all matches
  between elements and samples in `linkSampleData`. This increases performance,
  especially for larger data sets.
 

 Merge branch 'master'
 

 fix dgetrf fast_inverse
 

 Version bump in devel branch
 

 Added `jitter` parameter to `TIS()`.
 

 Fixed the incorrectly plotted image in README
 

 update unit test
 

 change 1:3 construction to seq() 

 Update propeller.ttest.R 

 Update normCounts.R 

 Update speckle_example_data.R 

 Update propeller.ttest.R 

 Update propeller.R 

 Update ggplotColors.R 

 Update estimateBetaParamsFromCounts.R 

 Update convertData.R 

 add unit tests
 

 Update README.md 

 v1.11.1 -- minor change in gene_set_enrichment() that provides more info
 

 correct a few class == tests
 

 bump
 

 Merge remote-tracking branch 'upstream/master'
 

 Rerun pkgdown
 

 Try adding an issue template to cut down on support questions to the issues
 

 Fixes #157

Also quell warnings about nobs.default
optimMsg was not being properly unlisted.
 

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 

 Add a exprs_values slot to the ZlmFit class.

Needed to maintain state in lrTest and bootstrapping.
 

 Add test RE: #158

unrelated: quell a couple warnings from lmer
 

 Fix link to MAST tag on support.bioconductor.org 

 bump to 1.1.5
 

 bump version number
 

 version bump before push
 

 Change box file link for embryo 3
 

 Add mouse gastrulation seqFISH data
 

 fixed Rd error
 

 minor
 

 alias hpar
 

 remove .rda from vignette and code/examples
 

 add allHparData() to example
 

 fix sentence
 

 update metadata.csv
 

 fix: separate tags with colon instead of comma
 

 Merge branch 'devel'
 

 fix gha deploy 2
 

 bump version
 

 fix errors
 

 updated to hpa 21.1
 

 fix tests
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 create a script in inst/scripts/ for Lee2019-data
 

 add .github to .Rbuildignore
 

 Update check-bioc.yml
 

 added interpro url; number of coorthologs and present taxa
 

 Bugfixes
 

 fixing bugs for version 3.0 and bumping to version 2.99.0
 

 Merge branch 'master' into devel
 

 finishing new functions and fixing colors
 

 ultimando función visualización pathways, y añadiendo nueva de creación de reports (wrap)
 

 separating plotVG function into nodes, edges and plot
 

 changing hipathia structure to make uniprot and GO terms be computed inside main hipathia function and creating DApathways function, to compute all comparisons of all datasets in a single function (wrap to do_wilcoxon and do_limma)
 

 fixed a bug of insufficient buffer
 

 meta.export
 

 Merge branch 'master' of git.bioconductor.org:packages/Rsubread
 

 update NEWS
 

 Merge branch 'update_Junker2014' into develop
 

 bump to 1.17.3
 

 Update RoxygenNote
 

 1.17.2
 

 Merge remote-tracking branch 'upstream/master'
 

 fix KYCG_loadDBs bug
 

 update vignette with the public workspace info
 

 updates to build site
 

 typos in new text
 

 Logo version bump
 

 0.99.7