Change version from 1.99.1 to 1.1.1 (1.99.1 never propagated so it's ok)
 

 set AnVIL version dep
 

 add api_reference_headers in Service spec
 

 update README
 

 add BiocCheck to tests
 

 Safe to call updateObject() on QFeatures objects

Starting with QFeatures 1.5.2, updateObject() works on QFeatures objects
so these objects no longer need special treatment.
 

 bump version
 

 add stage labels to circular legend
 

 version 22
 

 version 21
 

 version 19
 

 fixed loading cluster from config
 

 Come explanation on tweaking parameters
 

 changed the line
 

 updated version
 

 chnaged some lines
 

 Merge branch 'weights_fix'
 

 Updated AsCas12a
 

 Added new line
 

 chnaged one line
 

 changed one line
 

 changed man files
 

 changed vignette
 

 add enrichment for all predicted human proteins
 

 version bump 1.31.14
 

 Merge pull request #147 from Bioconductor/gitclone

update BiocCheckGitClone 

 update typo
 

 Added clustering algorithms
 

 version bump
 

 update BINARY_BASE_URL to https://bioconductor.org/pacakges

- access/.htaccess redirect on master.bioconductor.org to current
  binary repository location
 

 ade4 depend spec to help with Debian installs
 

 Fix typo in doc Rox source for refseq accessor 

 Merge pull request #1127 from mikemc/patch-1

Fix reference to deprecated function 

 Fix instructions for the `prune` option 

 committed changes locally
 

 version bump and NEWS update
 

 accept `bplist_error` as the argument of BPREDO

- add a new accessor `bperror`
- `bplapply` and  `bpvec` accept `bplist_error` as the BPREDO argument,
- update unit tests and vignette
 

 distinguish between pfam and smart links
 

 Standardise cset and encoding arguments; allow UTF8 and UTF-8
 

 use UTF-8 instead of UTF8
 

 Some unit tests for H5T functions
 

 Add copy to azcopy command
 

 requesting matrix package
 

 getCiprop working
 

 With up-to-date vignette
 

 Some explanation
 

 Plot full range of test statistics in plotNull
 

 Faster mixturer calculation
 

 Correct qwilcox
 

 Fix plotnUll
 

 Mistake in Fdr
 

 full np works
 

 Manparge for newly nadme fun
 

 Faster impl
 

 Documenting
 

 Choice for assumenormal
 

 Small changes
 

 Tryout
 

 No resamDesign if p-values given
 

 added the doc of SeqType
 

 bug fix: model not found error in line 64
 

 bump the version into 1.9.1
 

 Bump the version into 2.0.1
 

 Update README.md
 

 Fix title in rawrr bib entry
 

 v0.35 bpDist new filteringmethod
 

 improve anno_word_cloud()
 

 paper revision
 

 paper revision
 

 Merge branch 'master' of github.com:jokergoo/simplifyEnrichment
 

 Merge pull request #57 from krassowski/customisable-count_words

Allow users to customize the count_words behaviour 

 add genefilter to Suggests
 

 Update R-CMD-check.yaml 

 update actions
 

 update actions
 

 Update R-CMD-check.yaml 

 Merge branch 'master' of github.com:jokergoo/simplifyEnrichment
 

 Update R-CMD-check.yaml 

 Use VCorpus as SimpleCorpus does not allow for custom tokenizers

The previously used Corpus was creating a SimpleCorpus which takes
various shortcuts to boost performance (i.e. is missing functions and
does not complain if provided options that it does not support);
both SimpleCorpus and VCorpus are in-memory corpora
 

 limma 3.51.1

- Improve checking for incorrectly specified `contrasts` argument in
  contrasts.fit().

- Rerun case study in Section 17.4 of the User's Guide
  (time-course experiment with Agilent rat microarrays)
 

 Actually remove the mzdata files
 

 committed changes locally
 

 Delete epimutacions.Rproj 

 Update DESCRIPTION 

 version bump
 

 vignette edit cause it did not build on some systems
 

 Solved conflicts
 

 Updated readme
 

 New version, tests for plots of data with missing values
 

 Reorganize vignette
 

 Weird dbi error remains
 

 ebuilding reamde
 

 Warning and explanation when few categorical, constraining variables
 

 Update to the version 2.7.2
 

 fix bug in chr level in qc function to be
 

 Update workflow to Bioc 3.15
 

 Additional method documentation
 

 Add error handling to methods
 

 Remove -Wall C flag
 

 Update NEWS
 

 H5R unit tests
 

 Supress output from h5createGroup()
 

 Remove some print statements
 

 Subsetting H5Ref class
 

 writing working fairly well
 

 Add H5R_get_name
 

 Initial commit for writing object ref datasets
 

 implement reading/writing HDF5 object references in attribute

h5writeAttribute(object_to_reference, object, attribute_name) will write
a reference to object_to_reference into attribute_name of object.
Similarly, if attr is an attribute containing an object reference,
H5Aread(attr) will return an H5IdComponent of the referenced object.
 

 modifying vignettes (11)
 

 Fixed conflict
 

 R 4.0
 

 initPower parameter, and FAQ on samples on top of each other
 

 Bug fix missing values gaussian
 

 New roxygen version
 

 Star shaped features
 

 devel bug fix
 

 merged with upstream/master and resolved conflicts
 

 Update LICENSE.md 

 Added watch tags
 

 update
 

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

 Update maintainer
 

 runCommandline cleaning
 

 build_check 

 minor updates runWF fct
 

 clusterRun
 

 build_check; Improved running time when targets subset
 

 build_check; versionUP
 

 only one e-mail associated
 

 fix collate error caused by removing fgcz_helper file
 

 version bump and NEWS update
 

 do not output empty line with sink()

- improves 27f704689ef2601fdf4efd4f06e3bef616e8582a
- closes #171
 

 Update CreateAHubPackage vignette to upload to Azure instead of AWS
 

 Add screenshot place holders and update instructions for using R of local copy
upload
 

 Renumber
 

 Azure updates to vignette

  - command line option
  - R interface partially complete
  - shell of GUI
 

 Update http://s3.amazonaws.com/experimenthub to
https://bioconductorhubs.blob.core.windows.net/experimenthub/
 

 Version bump for AWS to Azure switch in makeMetadata function
 

 edit description, email
 

 gitignore
 

 Merge pull request #562 from lgatto/jomain

fix: fix issue in compareChromatograms 

 ci: change to R 4.1 and Bioconductor 3.14

- Change to older R/BioC version because package rpx is not available for R 4.2.
 

 ci: use new GH action

- Use newer format of the GH action.
- Bump version.
 

 Merge branch 'master' into devel
 

 Merge branch 'master' of git.bioconductor.org:packages/MSnbase into devel
 

 committed changes locally
 

 .
 

 80-character width limit
 

 verbose argumet in DRrefit and computeNormalChromosome
 

 thresholding fixed
 

 small cx_report improvments
 

 workflow fix
 

 Update version
 

 coverageOverRanges output order matches now input order
 

 update news and bump version
 

 update news and bump version
 

 update news
 

 update news and bump version
 

 fix a bug for rf method
 

 fix test
 

 bump to 1.13.3, another attempt to solve the C stack limit issue
 

 modifying vignettes (9)
 

 Fix DESCRIPTION 

 Merge remote-tracking branch 'upstream/master'

correction of identying sex.
 

 Merge pull request #45 from DanielEWeeks/master

Fix for data with missing probes 

 Fixing typo.
 

 subsetted object fix
 

 Fixed count interactions test
 

 Adjusted to allow all missing labels
 

 Added citation
 

 Fixed bug when some combinations are missing
 

 Install testthat as last package
 

 Added libnode-dev
 

 Added pandoc
 

 Added libcurl4-gnutls-dev
 

 Changed containers
 

 update
 

 fix bug when type in colData is factor

integtate_replicates function 

 fixing cran check
 

 main in plotEpistack
and horizontal bins label in plotBinning
 

 Add SystemRequirements: C++11 back to DESCRIPTION

The code base is using C++11 features and apparently some compilers
need to be explicitly told to enable those features.
 

 cells-method, events-method
 

 code cleaning
 

 minor plot improvement
 

 posterior to aposteriori
 

 Also install derfinderPlot from Github since regionReport 1.29.1 needs derfinderPlot 1.29.1 which is currently available only via GitHub
 

 Used biocthis::use_bioc_github_action("RELEASE_3_14")
 

 Used biocthis::use_bioc_github_action("RELEASE_3_14")
 

 include testthat 

 Add more comments related to the docker setup. Resolve #25
 

 Merge remote-tracking branch 'upstream/master'
to fix the test error reported in upstream
 

 modifying vignettes (7)
 

 modifying vignettes (6)
 

 Used biocthis::use_bioc_github_action("RELEASE_3_14")
 

 Used biocthis::use_bioc_github_action("RELEASE_3_14")
 

 Used biocthis::use_bioc_github_action("RELEASE_3_14")
 

 install github version of derfinderPlot for bioc 3.15
 

 v1.29.1
 

 Work-around https://github.com/lawremi/ggbio/issues/159
 

 biocthis::use_bioc_github_action("RELEASE_3_14")
 

 revert subscription check to affect all checked packages
 

 Merge pull request #586 from sneumann/fix/removeMzDataTests

Fix/remove mz data tests 

 Use mzML instead of mzData files in testing and vignettes
 

 Used biocthis::use_bioc_github_action(biocdocker = "devel")
 

 test with BioC 3.15
 

 Fix R version for BioC 3.15
 

 Disable gencode v25 tests since they have been failing frequently due to Gencode's ftp server
 

 updated version to 1.9.1 in NEWS
 

 Merge branch 'master' into 21Q4 

 finished 21Q4 changes
 

 refactor: update message for installing megadepth interactively

match message between interactive and non-interactive installation messages, so both pass tests
 

 Updated description
 

 BUG FIX: rangedDataToWig
 

 Modified approach to identify multimapping reads in Telescope
 

 Implemented minimum required overlap for the Telescope method
 

 addressed issue at https://support.bioconductor.org/p/9140582/
 

 version bump 1.31.12
 

 repair mishandling of description metadata in ALT fields
 

 doc: compiled docs for updateObject methods
 

 refactor: improve updateObject implementation
 

 fix: implemented an  method for  objects.
 

 document use of adjacency matrices
 

 bump version for Bioc 3.15
 

 new gh devel version
 

 Merge pull request #13 from ManonMartin/master

new hpar version 

 updated hpar version
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized BSseq instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 Pass serialized S4 instances thru updateObject()
 

 update figure
 

 remove phyloseq class
 

 update plot methods and mpse
 

 update MPSE function and convert phyloseq data to MPSE data
 

 speed up mp_cal_abundance
 

 update vignette
 

 update mp_plot_abundance and mp_plot_ord
 

 update show
 

 update mp_plot_dist
 

 update as.MPSE for biom class
 

 update news
 

 update otutree<- method
 

 update show