Fix link to https://support.bioconductor.org/tag/spatialLIBD/
 

 fix plot() and image() not always respecting dimnames
 

 v2.7.3 findpeaks_knn etc
 

 update estnoise_*() functions; add matter2-signal vignette draft
 

 add overlap arg to findbins()
 

 merge 2.6.3 bugfix
 

 update docs
 

 rename locmax_knn => knnmax()
 

 allow rowdist_at() to take matrix args for 'at'
 

 add profmem and memtime to deprecated
 

 deprecate asearch() and nnpairs() -- not really used
 

 add faster path for knnsearch() when data and query are the same
 

 fix convolve_at() bugs
 

 update convolve_at() to support matrix index
 

 add locmax_knn() and locmin_knn(); rm ... from locmax() and locmin()
 

 rename C func iCorr => iCor
 

 update enhance_xxx() functions
 

 add locmax2() and locmin2()
 

 fixes flow rate
 

 update the news file.
 

 modification flow rate anomaly removal
 

 Minor bug in geom_rect
 

 Replace logo URL
 

 Sigma is calculated on values before taking absolute value
 

 4.7.3; more kjohnson3 failures
 

 Preserve existing order of rows in *DataTable panels. (#658)

 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 add block_vector to normalization call
 

 Update Vignette
 

 Update README
 

 version bump
 

 Changed example to `dontrun` in igblast.Rd

--Changed `donttest` to `dontrun`in examples
--Roxygenised to igblast.Rd
 

 Adding \donttest to igblast to pass osx-arm64 check

--Added \donttest to examples in igblast.R
 

 Added conditions for skipping igblast on osx-ARM64

--Added skip_if() for osx-ARM64 to skip igblast functionality in testing
 

 Merge branch 'igblast-test' of https://github.com/rodrigarc/scifer into igblast-test
 

 Merge remote-tracking branch 'origin/devel' into igblast-test
 

 import from basilisk.utils

import `isMAcOSX()` and `isMacOSXArm()` functions from basilisk.utils package
 

 Added import basilisk.utils

-Added import basilisk.utils for roxygen2 usage
 

 fix basilisk conditional for linux

`basilisk.utils::isLinux()` function did not exist for R 4.2. Changed for a more general to check the OS in case of Linux
 

 edit text from vignetter for igblast
 

 create windows environment

try to overcome errors in windows due to lack of igblast on bioconda channel
 

 Moved dnaio to pip install in basilisk env

-Added pip install dnaio to basiliskEnvironmnet for testing environment compatibility with windows
 

 Add igblast db directory tree to walkthrough

- Added explanation about where in the directory tree databases should be located
- Changed eval=T in markdown
 

 Added additional `.fasta` file for testing

-Add `.fasta` file with 8 sequences for testing igblast
 

 Updated Bioconductor Style #2

-Bioconductor code style applied to .Rd files with Roxygen2
 

 Add zstandard dependency to env

-Add zstandard==0.22.0 dependency to basilisk env.
 

 Add zlib-ng dependency env

--Add zlib-ng==0.4.3 dependency to basilisk env
 

 Add wheel dependency env

-Add wheel==0.43.0 dependency to basilisk env
 

 Add pycparse to dependency env

Add pycparser==2.22 dependency basilisk env
 

 Updated package name isal

- python-isal==1.6.1 dependency for basilisk env.
 

 Removed comma causing error

Removed a comma causing an error when loading basilisk env.
 

 Revert "Updated Environment Dependencies"

This reverts commit fe24a4c4f36b875ec7edd46ebe0b4d5f71049981.
 

 Fixed deprecated tidyselect syntax

-Changed .data$.id conflicted syntax with fixed global variable
 

 Corrected Test functions for igBlast

- Updated conditions for error messages when checking directories before running igblast
N.B.  When loaded pkg(here) sets directory to "$/scifer/" so here(db_dir = "") does not trigger the stop conditional because the db_directory is "$/scifer/" .
- Updated test function conditions for igblast
 

 devel version bump

- 2 commits were added
 

 delete or move unnecessary filles

- removing extra test data
- removing igblast test function
- moving python igblast script
 

 Function for IgBlast

Added function for igblast via basilisk
Arguments for the function paths to database and fasta files.
Needs updated markdown comments describing the function
Needs function optimization
 

 basilisk.R file for creating environments

Code to create the correct environment for igblast 

 fix error

for some reason the python wrapper needs to be sourced prior running it
 

 add KIMDB database to test
 

 updated igblast standalone version
 

 Update README.md

edit description of parameters to make it clearer 

 Updated and moved R/Bioc versions in Readme

--Moved R & Bioc versions to above installation and under author and maintainer section. Improved language
 

 Added additional walkthrough_link to README

-Added additional reference to the walkthrough vignette
 

 Updated force = true condition for installation

-Adding `force = TRUE` to installation segment if the user has older packages already installed
 

 Updated introduction to default parameters

- Updated introduction for default parameters: spelling
 

 Generalized probe1 argument

--Changed argument placeholder to "my_probe_channel_1"
 

 Removed lines 211 & 212

--This code runs without error or warning
--removed lines containing arguments (211-212)
 

 Updated version

--Updated version to 1.7.3
 

 Explicitly stating default parameters

- Added explanation of default parameters with recommended values for macaca mulatta, mus musculus, and uncertain experiments
 

 Updated installation instructions

-Added code installation instructions for installing from bioconductor
-Updated text defining differences between github and bioconductor version installation
 

 Update README.md

add badges for master branch only 

 Eval=T chunk works for IgBlast

-IgBlast Eval=T code chunk runs in scifer_walkthrough
 

 Updated walkthrough includes igblast

-Added igblast to scifer_walkthrough.Rmd vignette
 

 Updated Threads argument conditions

-Updated conditions for testing igblast to return error arguments
-Checks for the directory path
-Added threads argument
-Currently catches `NULL` , `length()==0`, `NA` and `""`
- Suspicion that `is.null(db_dir)` doesn't do anything and could be replaced by  `length(db_dir)==0`
 

 Shortened path in system.file

Shortened local path within igblast.R script example
 

 Python-zlib-ng dependency

--Add python-zlib-ng==0.4.3 dependency to basilisk env to enable package install
 

 Add xopen dependency to env

-add xopen==2.0.1 dependency to basilisk env
 

 Add setuptools to basilisk env

-Add setuptools==70.1.1 dependency to basilisk env
 

 Add pip dependency to env

-- Add pip=24.0 dependency to basilisk env
 

 Adding isal to env dependency

- Add isal==1.6.1 dependency to basilisk env
 

 Updated Env Dependency cffi

Added cffi==1.16.0 dependency to basilisk env.
 

 yulab-msg
 

 update
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 update bioc version
 

 Merge pull request #758 from sneumann/quick_fix

small fixes 

 refactor: dump all data export functionality from xcms

- Remove the data export functionality (`saveResults()`) from *xcms* as it will
  be implemented (in a more structured and cleaner way) in the new *MsIO*
  package.
 

 new function to mark nodes according to their position in BowTie.
 

 removed a bug on macOS
 

 accelerated overlapping calc.
 

 Added support for matrix multiplication on already-initialized pointers.
 

 Exported all utilities to directly operate on a tatami pointer.

This means that developers don't have to carry around the original
matrix if they just want to do some preprocessing on the already
initialized matrix prior to entry into their C++ code.
 

 Fixed a bug in the function cvt_id.
 

 Earlier check in estpis
 

 Adding back txdbmaker dependency and updating the Maintainers' info 

 Merge branch 'devel' into switch-from-rmysql-to-rmariadb 

 Version bump in devel
 

 Export .selectInputHidden (#656)

* Export .selectInputHidden

* document newly exported function

---------

Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com> 

 modification
 

 modification
 

 thesisData upload
 

 modification
 

 file move
 

 file move
 

 data update
 

 Merge pull request #16 from systemPipeR/devel

prepare for new release 

 deprecate github install
 

 fixed a bug in donotsort paired-end
 

 Bump version to trigger reinstallation to match new basilisk.utils.

Specifically, basilisk.utils (1.17.1) is switching to the Miniforge
installer, so we want to retrigger installation of all environments on
the build machines to make sure everything works.

Updated vignette to reflect the use of Miniforge.
 

 Clarified documentation around paths= for local Python packages. (#39)

 

 Merge pull request #38 from Bioconductor/channel-licensing

Commented on the licensing problems with the defaults channel. 

 Switch over to the latest miniforge by default.  (#12)

This involves some fiddling to get it working on Windows, mainly so that the
installer accepts the installation path without silently failing.

Users can still switch back to miniconda via the BASILISK_USE_MINIFORGE=0
environment variable, at least for now. 

 QDNAseq 1.41.3
 

 Make it possible to disable plotting in test
 

 Merge tag '1.41.2' into develop

QDNAseq 1.41.2
 

 fix build error
 

 fix errors
 

 add orcid
 

 added co-author / co-maintainer
 

 assign fitType first
 

 fix missing brace
 

 update mp_plot_diff_clade to compatible with ggnewscale >= 0.5.0
 

 version 8, further seq-ology.
 

 Add a CONTRIBUTING.md (#27)

The CONTRIBUTING.md file is based on the following template:
https://github.com/auth0/open-source-template/blob/master/GENERAL-CONTRIBUTING.md
 

 fix: selectSpectraVariables to not drop peaks variables

- Ensure `selectSpectraVariables()` for `MsBackendMzR` is not removing peaks
  variables `"mz"` and `"intensity"` by default.
 

 Add figures to Readme
 

 Merge branch 'devel' of github.com:khazum/ccImpute into devel
 

 Update README.md 

 Update README.md 

 bug fix: extract package only in checkVigSuggests
 

 Address some notes/warnings in BiocCheck and R CMD CHECK. Mostly, make sure necessary imports from methods are available
 

 unify param def (#603)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 Fix addAlpha (#612)

 

 Minor fix to convertToBIOM (#607)

 

 QMP example data #470 (#597)

Co-authored-by: Shadman Ishraq <shadmanishraq2@gmail.com.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: TuomasBorman <tvborm@utu.fi> 

 import functions and ranks (#590)

 

 fixed legend in cc_dotplot
 

 Change order of label checking. NA labels should be checked before checking for label dimensions.
 

 Add codecov
 

 Bump package version from git merge conflicts
 

 Bump z in version
 

 Update version
 

 Move computation of logcounts to ensure that tests work as expected.
 

 Update test message
 

 Update documenation language for cells/spots/observations
 

  Addresses #2: Add checks for NA labels.
 

 Add check for label quantities compared to number of observations
 

 Change collapse stop/warn message handlers to a single function
 

 For set_names_* functions, the errors should be considered internal. Also, checks for NA labels and label dimension should be added to `check_labels()`
 

 Remove extra file in /tests
 

 Update pkgdown.yaml

Change bio conductor version 

 fix overview example to match readme
 

 Remove imports that are not used
 

 Update documentation for assay and dimred
 

 Rename demo to nonspatail example
 

 fix minor bug in do.call
 

 Catch error where mixed_compatible labels aren't classed as discrete
 

 Fix name of warning handler
 

 Add tests for label utilities and concordex function
 

 Significantly declutter man/ pages. Remove entries for internal utilities
 

 Add tolerance to `is_integer`
 

 Update Readme and basic demo
 

 Update contributors list (#136)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Update plotAbundance.R (#139)

 

 Update MARGIN param (#133)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Fix ndetection (#137)

 

 edit RCy3 chunk
 

 Corrected handling of svalues with Wald Test
 

 ImageJ -> Fiji updates related to https://github.com/LieberInstitute/visiumStitched/issues/1
 

 save the full meddra data
 

 fix error: in correct index length
 

 change pseudo count for ratio matrix
 

 refactor: update unit tests
 

 fix: issue with providing nested confounder
 

 refactor: update unit tests
 

 fix: issue with providing nested confounder
 

 bumped to 6
 

 Merge branch 'release/1.41.2'
 

 BUG FIX: poolRuns() would produce an error [#112]
 

 Merge tag '1.41.1' into develop

QDNAseq 1.41.1
 

 deprecate beachmat::whichNonZero (#111)

* deprecate beachmat::whichNonZero 

 add help video playlist
 

 4.7.1. Fix kjohnson3 failure, Note lost braces, miscell minor
 

 Bumped version to push upstream
 

 Bumped version number.
 

 all.rd removed
 

 S removed from attributes
 

 S and Sprime fixed
 

 solves latex error build problem
 

 Merge the logo

Merge branch 'main' of https://github.com/AnnaLaddach/CatsCradle
 

 revised for resubmission
 

 Improve vignettes
 

 Merge pull request #110 from hpages/devel

Compatibity with DelayedArray 0.31.7 

 require SparseArray >= 1.5.18 instead of 1.5.19
 

 bump bioc version in action
 

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

 Update to v1.20.1
 

 Update to v1.20.1
 

 vignette updates
 

 Merge remote-tracking branch 'upstream/devel' into 1.7.1-devel
 

 GHA
 

 Implement GO-sqlite file checking before opening

Also uses RSQLite::SQLite() instead of DBI::dbDriver("SQLite") to open databases
 

 Update github workflow biocversion
 

 Update recent commits to sync with main
 

 New namespace, remove plotting exports
 

 Remove obsolete files
 

 version bump 0.99.30
 

 fix getHSDSFileList
 

 Added a new NEWS entry.
 

 Pass along extra quickCluster arguments when using block=. (#109)

 

 Bioconductor review
 

 Fix retrieveMembranePositions(), update feature names
 

 Version bump after bugfix
 

 Bugfix in addDiffStatus
 

 version bump 1.17.11
 

 Typo vanderdoes
 

 Solve problems with experiment and fov variables in eng data
 

 version bump 1.17.10
 

 version bump 0.99.29
 

 version bump 1.15.1
 

 update vignette
 

 use AnVILGCP imports
 

 Update README.md
 

 Version bump after bugfix
 

 Still a problem with the vignette builder?
 

 Version bump
 

 Trouble from do.call(cbind, args) when args has names
 

 What if some transcript spots are outside the bbox of colGeometry
 

 Fixed a bug in featureCounts on BAM files with headers ~ 2GB
 

 SparseArray 1.5.25

Small improvements to the vignette.
 

 v1.41.1
 

 Some R CMD check issues from plotting rowGeometries
 

 Major change to plotGeometry to plot multiple geometries at once and plot transcript spots. Added plotTxBin2D.
 

 Removed deprecated arguments and addressed R CMD check issues
 

 Implemented and tested aggregate method, closing #27
 

 R CMD check issues
 

 Unit tests for aggregating transcript spots
 

 Export functions for Voyager
 

 Added aggregate and split
 

 minor fix
 

 Small changes for XOA v3
 

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 

 Need to switch branch
 

 pull changes and resolve conflicts

Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel

# Conflicts:
#	R/coerce.R
 

 Merge branch 'release/1.41.1'
 

 typo in version
 

 Disable unit test for Bug #112
 

 GHA: modernize - take 1
 

 Fix markup typo in help("exportBins")