Protect against nested ALTREPs when creating lazy rows/cols.
 

 Reoxygenated.
 

 Allow coercion of DF column names to a safer variant.
Updated tests to check coercion.
 

 Updated tests for the DF-maker functions.
 

 Flipped makePerFeatureDF to use lazy evaluation scheme.
Renamed gg functions to refer to each dimension.
Docfixes, updated vignette for new function names.
 

 Reoxygenated.
 

 Support data extraction from alternative Experiments.
 

 Added basic function to create column-based DF from SCE.
 

 updated
 

 Fix data.table issue #42
 

 Update .travis.yml 

 make default run_cicero not silent
 

 Merge pull request #64 from vdsukhov/master

Fix bug in collapsePathways 

 version bump (one tailed tests)
 

 change the style of error handle.
 

 adding withDimnames=FALSE to assays calls
 

 correct bug untar
 

 Merge branch 'develop'
 

 Merge branch 'develop'
 

 Fix issue created by .warn_once in DetailedAnnotationTrack. Changes strand methods. Added some more tests.
 

 Bumped version and date, reoxygenated.
 

 version bump
 

 fix a issue of vignette when visit ebi proteins api.
 

 No need for ifelse as logicals are essentially 1/0 

 Add while loop in basics_sim for zero colsums (#158)

version 1.9.19 (2020-02-16)

Adds a while loop in BASiCS_Sim to ensure it doesn't fail if some
generated cells have zero counts.  

 Code cleanup. Replace sapply with vapply
 

 Clenaup of code (tab to 4spaces)
 

 Fix links in rREADME
 

 Rewrote values replacement method, clenaup AllClasses
 

 Added tests for subseq and chromosome
 

 [skip travis] Updaded links in README.
 

 Edited readme
 

 bump
 

 fix test case
 

 add 'trans' argument to optionally override the transformations from gatingML file with scales info recorded in yaml #79
 

 parse the missing tags from yaml #79
 

 Realize view in diva_to_gatingset before save_gs
 

 Merge branch 'master' of github.com:RGLab/flowWorkspace
 

 Handle deprecated "link" option to save_gs
 

 Merge branch 'master' into devel
 

 add overwrite=false to copy methods and allow 'move' option for subsetted cytoframeview
 

 Fixed conflicts in version change
 

 cleaning dependencies - plyr
 

 Removing dependencies - dplyr
 

 Added check to confirm files entered are real
 

 Description syntax error
 

 Revert "updating version for bioc release"

This reverts commit 2b85cf71fbbb07d0ceea9ba22071f9a4beb797d8.
 

 Travis 8
 

 Travis 6
 

 travis 3
 

 Updating Travis
 

 PRS pathway names
 

 update citation
 

 Merge pull request #28 from xiangpin/master

support multi phylogeny in phyloxml and extra information 

 Add git and docs URL to the description 

 man of write.beast
 

 man of root-method
 

 add multi phylogeny in examples
 

 update makefile
 

 if yscale is set do not scale y 

 fixing incorrect links
 

 Merge pull request #273 from brj1/master

Unrooted layout fix 

 added new layout 'ape' which is a copy of the 'unrooted' type in ape::plot.phylo
 

 geom_highlight
 

 merged; fixed example; changed Brad Jones email
 

 rename version 1.1.2
 

 uniprot2go windows debug
 

 merge bioconductor /upstream changes and version bump
 

 rowr dependency removed.
 

 More unit tests added.
 

 Fix saving file name for preliminary object.
 

 update release date
 

 Expand SampleRes to DownsampleResolution, downsample.res to downsample.resolution
 

 Rename "statistics" tables to "data" tables
 

 panel.color is a character vector, not a list
 

 ignore files produced by unit tests
 

 rename ReducedDimPlot -> ReducedDimensionPlot
 

 fix and restore coverage
 

 Expanded slot names for selection aesthetics.
 

 Remove backquotes.
 

 Reoxygenated.
 

 update unit tests
 

 Revert "Rename: ReducedDimPlot -> ReducedDimensionPlot"

This reverts commit 4256d63c79fccc45a084f1a4c388170b5dd2f33d.
 

 fix dimnames in test setup
 

 revert a1594ee3
 

 Convert contract descriptions to subclass expectations.
Moved generateTable docs to separate file.
 

 update unit test
 

 deparse the individual elements of x[[.heatMapColData]]
 

 process syntactically invalid column names safely when ordering heatmap columns
 

 Cleaned up landing page documentation.
 

 Upgraded the custom vignette as well.
 

 Updated configuration vignette.
 

 Renamed RowStatTable to RowDataTable.
 

 Renamed ColDataPlot to ColumnDataPlot.
 

 Renamed FeatAssayPlot to FeatureAssayPlot.
 

 update basic vignette to be more open about custom panels
 

 Describe individual global panel options
 

 update NEWS
 

 typo and fix check of assay row centering
 

 set panel global options following the knitr::opts_chunk framework
 

 Reoxygenated.
 

 Bugfixes to custom panels, further methods to clean up UI.
 

 Auto-detect arguments from the custom function definition.
 

 Merge remote-tracking branch 'upstream/master' into custom
 

 update heatmap tests; prefix ComplexHeatmap and circlize commands; safe acccess to syntactically invalid column names
 

 Simplified heatmap code for clearer responsibilities.
 

 Broke up heatmap-generating code for easier reading.
 

 Fixed heatmap code to work with sparse assays.
 

 Added preliminary tests for new custom-class creators.
 

 Added observers to respond to custom UI elements.
 

 Initial attempt at a class-generating function.
 

 Simplified heatmap code for clearer responsibilities.
 

 Broke up heatmap-generating code for easier reading.
 

 Fixed heatmap code to work with sparse assays.
 

 Standardized doc file name for Table classes.
 

 exclude render from coverage
 

 cover .exportOutput for Table
 

 cover outputs_general.R
 

 Doc fixes
 

 Documentation syntax
 

 Protect against case of missing 'se' in iSEE().
 

 Bugfix for missing dimnames in underlying assay matrix.
 

 Merge pull request #353 from iSEE/outputs

Saving outputs as PDF/CSV 

 Merge branch 'outputs' of https://github.com/csoneson/iSEE into outputs
 

 Merge branch 'master' into outputs 

 Reoxygenated.
 

 Fixes to docs and imports to pass CHECK.
 

 Merge pull request #354 from iSEE/kevinrue-patch-1

Update issue templates 

 Update issue templates 

 More balanced distribution of options in dropdowns.
 

 Removed the rendering from the modal set-up.
 

 Fix to ensure only relative file is zipped.
 

 Merge pull request #352 from iSEE/com

badge links to travis-ci.com 

 Merge pull request #351 from iSEE/pkgdown

use workaround at https://github.com/r-lib/pkgdown/issues/1206 

 Merge pull request #349 from iSEE/cleanup

restore dpl v1 travis option 

 Merge pull request #348 from iSEE/deploy

fix new travis defaults 

 Removing data download from vignette
 

 updated
 

 Updated NEWS file for version 1.3.4 .
 

 Fix size of pdf output settings to use the given width and height values instead of the "USr" format.
Fixes in plot_cnv() when using observation groups with 1 or 2 cells.
Fix checks in plot_cnv() of references for when subclusters are not defined in the object.
Fix (sub)cluster definition when an annotation only has 1 cell (although this should probably be avoided).
 

 syntax fixes for BioC
 

 User requested deprecation
 

 Merge pull request #36 from huerqiang/master

change Category labels from ID to Description 

 change `ID` to `Description`
 

 Merge pull request #35 from huerqiang/master

fix function `prepare_pie_data` 

 fix function prepare_pie_data
 

 update readme
 

 clean up code
 

 Merge pull request #34 from huerqiang/master

add cnetplot.compareClusterResult() 

 add geom_node_text
 

 add theme(legend.position="none")
 

 add if(is.null(dim(y)) | nrow(y) == 1), if(ncol(ID_Cluster_mat2) > 4)
 

 delete "p <-"
 

 Merge pull request #29 from huerqiang/master

add pie_scale, legend_n 

 change the default layout
 

 add pie_scale param in emapplot.enrichResult
 

 delete n param in emap_graph_build()
 

 add legend_n param
 

 import scatterpie
 

 Merge pull request #27 from huerqiang/master

add node label 

 add return
 

 add pie param
 

 delete "else"
 

 delete group param in scatterpie::geom_scatterpie
 

 deleate group param
 

 fix a bug for one_line_y_union
 

 fix function emapplot.compareClusterResult for nrow(y_union) == 1
 

 Merge pull request #1 from YuLab-SMU/master

合并 

 fixed some bugs
 

 fix function graph_build
 

 add graph_build function
 

 change the value of "ID_Cluster_mat$radius"
 

 Merge remote-tracking branch 'upstream/master'
 

 fixed warning msg
 

 nothing
 

 add "import clusterProfiler"
 

 add emapplot.compareClusterResult function
 

 update retry
 

 Bug fixes. Bump to version 1.1.6.
 

 Merge branch 'master' of github.com:seandavi/BiocPkgTools
 

 fixed mislabeled context() in getPackageInfo unit test
 

 fix generic error
 

 debugging vignette issue 2
 

 add note on errors connecting to db
 

 Bumbed version after adding bunch of tests.
 

 fixed test for .import.bam.alignments
 

 test .import.bam.alignments
 

 Added small bam file for testing only.
 

 fixed issues in man pages
 

 Added missing entries in man and NAMESPACE
 

 Remove C++11 requirement
 

 Tweaks for coping with UTF-8 file paths
 

 fix conflicts
 

 bugfix in converting FCs to log2FCs in TranslatomeDataset
 

 cleaning up reduce/disjoin internals - cleans up disjoin cases when an expansion occurs.
 

 Reoxygenated, bumped version and date.
 

 Unname vectors in merged colData after aggregation.
 

 Merge pull request #31 from markrobinsonuzh/cleanup_branch

Cleanup branch 

 fix horizontal lines
 

 Updates for more stringent SE assignment.
 

 Make ZIP to be compatible to 2 X 2 combination matrix
 

 version 1.9.15 (2020-02-16)
- Use expect_equal in scran test (now all suitable tests)
- Minor change in `test_differential_test_reg.R` to use 3 instead of 2 decimal
points. This hopefully avoids issues associated to a bug in `round`. For details
see: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17668
 

 update version number to 2.1.8
 

 untrack .so and .o files
 

 16 Feb 2020: limma 3.43.4

- voom now checks explicitly for NA or negative counts and gives an
  informative error message.

- Cleaning up of internal code to avoid partial matching of function
  arguments, attributes or list component names. The automatic package
  tests are now run with the warnPartialMatchArgs,
  warnPartialMatchAttr and warnPartialMatchDollar options all set to
  TRUE.
 

 version bump
 

 Merge pull request #6 from Itagliaf/master

Fix in wrapper 

 Fixed wrapper to write all the graphs on a single pdf
 

 Added if-else to avoid creation of graphs that need the values from
the compendium
 

 Minor docfixes, reoxgyenated.
 

 Added the colLabels concept for storing column labels.
 

 Removed unnecessary setting of SF names.
 

 Docfixes.
 

 Stripped out tests for defunct methods.
 

 Updated updateObject to shift size factors.
 

 Began deprecating the spike-in methods.
 

 update to v1.2.4
 

 Update library.bib
 

 Update version for pre-release v2
 

 Merge branch 'master' of https://github.com/chrischen1/GNET2
 

 Merge pull request #15 from chrischen1/master

add force_split option 

 Merge pull request #13 from chrischen1/master

update 1.3.2 

 Update README.md 

 Merge pull request #10 from chrischen1/master

update docs 

 Merge pull request #9 from chrischen1/master

merge bioC version 

 Merge pull request #8 from chrischen1/master

Fix several conditions that may cause error in tree construction. 

 Merge pull request #7 from chrischen1/master

Package accepted by bioC-devel. 

 Merge pull request #5 from chrischen1/master

first version submitted to bioC 

 Reoxygenated, bumped version and date.
 

 Forgot to add rownames for Bach.
 

 Reoxygenated.
 

 Pull down genomic coordinates.
 

 keep seqlevels in mapToTranscripts()
 

 vignette: add purpose of the package
 

 fix conflicts
 

 fix conflicts
 

 fix conflicts
 

 fixed regression in combineIntoModstrings()
 

 fix conflicts
 

 fix conflicts
 

 add previous commits
 

 changed from KEGG to KEGGREST
 

 changed from KEGG to KEGGREST
 

 changed from KEGG to KEGGREST
 

 Link Sscrofa11.1/susScr11 to GCA_000003025.6 instead of GCF_000003025.6
 

 Yet more doc clarification about list inputs.
 

 Added tests for multiBatchPCA's new weighting mode.
Plus bugfix for errors.
 

 Updated tests for more thorough single-input checks.
Testfixes to address inequality of median inverse/inverse median.
 

 Pass BPPARAM to calcAverage for rescaling factors.
 

 updated the code for getDatabase() to allow downloading data from any location provided by /data/gene_database/