update Leonardo, Dockstore service md5 sums
 

 clean return value of gsutil_ls()

- seems like this is a capture of a directory listing, including
  formatting; strip the formatting and blank lines
 

 separate out check inputs function
 

 rm BACKEND arg
 

 use github actions
 

 travis devel bioc
 

 consolidate tests for matrix in R4.0
 

 Pull from BioC after version bump
Merge commit '875b51724c5f099864ba0bdc750a7be491df0013'
 

 consolidate tests for matrix in R4.0
 

 rm dplyr dependency
 

 version bump
 

 checking number of selected rows on row profile start
 

 Update appveyor.yml 

 Update README.md 

 Update README.md 

 Proper image link
 

 update README
 

 version bump to 1.3.1 for Bioc.
 

 Updated Description
 

 Merge updates from the Bioconductor (release 3.11), version number to 1.3.0 for Bioconductor sojourner develop branch.

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 

 diff, merged and tested Dcoef.Helpers.R. The commented out functions was clapsed in the master branch.
 

 (re)merged helperFunctions()
 

 - moved plotComponentTrackOverlay() to selComponentTracks() in sojourner.pro;
- tested and further modifications on msd() and plotTrack()
 

 diff and merged msd() function (for exporting msd.track vs msd_track etc).
 

 (re)move merging added pro functions
 

 Prepared files for merging:
- renamed Dcoef_Helpers, Plotting_Helpers so it gets diff with the develop when merging.
- renamed plotIndividualTracks so it won't get compared when merging.
- kept compare_RT_CDF.R, plotLocalizations.Density.R, plotTrackOverlay.Dcoef.R unchanged so it won't get compared when merging.
- updated help docs and namespace
 

 (re)moved bootstrap, fitCDF, getCI, hmmTrackll, and selComponentTracks to sojourner.pro.
 

 fixed plotLocalizations.Density(), plotTrackOverlay.Dcoef()
 

 updated sojourner GitPages website
 

 Add readTrackMate() function
 

 resolved Merge conflicts
 

 resolved Merge conflicts
 

 resolved Merge conflicts
 

 resolved Merge conflicts
 

 Update Bootstrap_fitRT.R
 

 Merge conflicts
 

 Namespace and Bootstrap_fitRT.R export fixed.
 

 Fixed Bootstrap_fitRT.R to export multiple functions.
 

 Merge conflicts of plotIndividualMSD().

Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop

# Conflicts:
#	R/plotIndividualMSD.R
 

 A series of functions to calculate 1-CDF of trajectory dwell times, boostrap the data (resample) and fit all the boostrapped data sets with multi-component exponential decay model to calculate averaged residence time and the standard deviate.
 

 Fixed a bug of plotTrackOverlay.Dcoef() when there is no track left for certain images after R sqaure filtration.

Modified plotLocalizations.Density() to plot 2 kinds of localization plots for each image stack, one with square-shaped bins colored based on number of molecules in each bin, the other with each molecule as a dot colored base on local density of molecules. Also added an option to customize color for the dot plot.

Modified plotIndividualTracks(), with options to sort tracks by dwell time, diffusion coefficient, or R square of MSD fit, also with options to add or not add legend on each panel.

New function plotIndifidualMSD() to visualize correlation of MSD regression error (R square) and the corresponding diffusion coefficient. This function can also plot all the individual MSD fits for visualization and diagnosis purpose.
 

 Merge branch 'develop' of https://github.com/sheng-liu/smt-beta-0.3.9.1 into develop
 

 plotTrackOverlay.Dcoef() fixed "argument to 'which' is not logical" error; nuclei background pixelated.
 

 plotTrackOverlay.Dcoef() fixed "subscript out of bound" error when there is no track left for a data file after filtration
 

 fixed import command
 

 Diffusion map analysis support added: diffusionMap.R. Could not document() with roxygen2 and could not build package.
 

 set .plotNucTrackOverlay() to condition on the input data to adjust for "color" statement differences.
 

 rebuildTrack reconnects segments along with statistics.
 

 Adding functions used for segment generation that will be used for hmm in the future.
A single function (convert.abtrackll) is added for helper functions
 

 Description update
 

 fix %% by 0 error
 

 Description update
 

 Fixes #57

   - version bump for Leonardo's PR
 

 Merge branch 'suggest_styler_over_formatR' of https://github.com/lcolladotor/BiocCheck into lcolladotor-suggest_styler_over_formatR

Conflicts:
	NEWS
 

 Merge branch 'add_pr_template' of git://github.com/lcolladotor/BiocCheck into lcolladotor-add_pr_template
 

 Merge branch 'grimbough-dontrun'
 

 minor changes to avoid merge conflicts
 

 Respond to the PR review

This commit does the things outlined at https://github.com/Bioconductor/BiocCheck/pull/88#issuecomment-630921073. That is:

* Removes any `biocthis` mentions.
* Uses CRAN links for `styler`.
* Fixes a typo.
* No longer bumps the version number to avoid merge conflicts with other BiocCheck-a-thon pull requests as suggested on Slack.
 

 v1.25.1 -- Resolve https://github.com/Bioconductor/BiocCheck/issues/57

This commit resolves https://github.com/Bioconductor/BiocCheck/issues/57
by updating the `handleMessage()` calls after the formatting check
fails. Instead of mentioning `formatR`, these messages now refer to:

* `styler`,
* `biocthis`,
* the `BiocCheck` vignette.

Furthermore, the `BiocCheck` vignette section on formatting still
mentions `formatR`, but it now also mentions in more detail:

* `styler`: how to install and run it
* `biocthis`: as a companion to `styler` with code how to run it
(but not install it since it's optional and the install instructions
will hopefully change soon once this package is submitted/reviewed).
* a quick overview of the differences between `formatR` and `styler`,
though this is mostly done by highlighting current limitations of
`formatR`.
* how RStudio Desktop's `Reformat code` button (under the magic wand)
can help break long lines which is something that `styler` cannot do
as discussed in more detail at
https://github.com/r-lib/styler/issues/247. `formatR` can do this,
but personally, the fact that it broke valid R code in some of my
packages made me trust its output less.

The NEWS and DESCRIPTION files have been updated accordingly.
 

 Bugfix when input data is a SummarizedExperiment. Corresponding unit test added.
 

 Delete file

Moving to bug sig 

 version bump
 

 version bump
 

 update NEWS file
 

 add testthat to Suggests
 

 version bump
 

 Allow pointing to different API 

 Fix typo and remove uneeded tests
 

 findKNN, select = "all" preceed / follows width on subject, not x
 

 helper and unit tests for findKNN select = "all"
 

 Documentation changes for findKNN and assorted fixes
 

 Merged with master branch
 

 Changes to findKNN() + unit tests
 

 simple unit tests and debugging 0-length cases
 

 Change to defaults

- in findKNN, changed from k=5L to k=1L
 

 fix the issue for new paste output.
 

 Merge branch 'RELEASE_3_11'
 

 Fixed package name replacement in Makefile.
 

 bump and news
 

 fix vers num
 

 Avoid memory explosion from storing all pairwise log-FCs.
 

 Simplified plot*Distribution functions to use matching calls,
as mismatches between scores/deltas and calls makes little sense.
Renamed scores/deltas.use= into references=.
 

 Fixed coloring of pruned calls in delta plot.
 

 Organized plotting tests into those for scores and deltas.
 

 Streamlined delta distribution plots by removing cut-offs,
instead plotting the pruned labels in a different color.
 

 Added separate, streamlined function to plot the deltas.
 

 Reoxygenated for example.
 

 Patch over odd matrix zero-subsetting behavior.
Fix to classic markers example.
 

 Added tests for getClassicMarkers, minor arg fix.
 

 Reoxygenated.
 

 Switch examples to use .mock*Data functions for brevity.
 

 Report the reference of origin for each column of a combined 'scores'.
Remove unnecessary code to merge the marker lists.
Cleaned up combining documentation.
 

 Bumped version and date.
 

 changing NAMESPACE file
 

 bump version number
 

 added version update to pset conversion, otherwise already converted psets loaded by downloadPSet would be converted again (and fail)
 

 version bump
 

 fix version check warning
 

 Removed RangedData functions as they are now gone from IRanges.
 

 update version
 

 Fixed boundary issue for champ.refbase.
 

 Merge pull request #54 from lgatto/master

feat: new countFeatures aggregation function 

 test: add colCounts() unit tests
 

 feat: new countFeatures aggregation function
 

 Merge pull request #83 from PeteHaitch/master

Fix table in vignette 

 Merge pull request #82 from snystrom/nearest_distance_doc_edit

Quick fix to join_nearest_distance docs 

 Mention rowSubset usage in vignette.
 

 Bumped version and date, updated NEWS.
 

 Added the rowSubset utility for storing row subsets.
 

 add automatic conversion method
Make the generic function more generic.
add document.
 

 Update version bump
 

 prepend extra meta info to wsp file generated by gs-to-flowjo
 

 Handle spaces in paths in gatingset_to_flowjo
 

 Add docker image version match to gatingset_to_flowjo
 

 Let gatingset_to_flowjo use binary or docker
 

 add skip_faulty_gate arugment to flowJo parser. #96
 

 Make docker availability check work with Windows
 

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

 Move coercions from Hits to DataFrame and data.frame to S4Vectors package
 

 alter computeInfRV function for mean and var
 

 Bump version.
 

 Merge branch 'shiny-updates' of https://github.com/pablo-rodr-bio2/GSVA into pablo-rodr-bio2-shiny-updates
 

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 

 update vignette and add message asking to look at the doc if curl not installed on Windows
 

 missing header file for countFastq
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Update dev/ files
 

 Update dev/ files
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5
 

 Bumped version and date, added extra contributors.
 

 Cleaned up Zilionis-related scripts:

- Moved them into the right subdirectory.
- Use more appropriate functions for data loading.
- Retain more of the published metadata, where sensible.
 

 removing monocle and igraph dependencies
 

 set tidy=TRUE as default in predictSmooth, #51
 

 add tidy argument for predictSmooth, #51
 

 Added travis build badge
 

 sycning w/ bioconductor Merge branch 'master' of git.bioconductor.org:packages/multiMiR
 

 Add warning message about target IDs 

 Merge branch 'master' of git.bioconductor.org:packages/isomiRs into gitdev
 

 Updated documentation
 

 change the normalization method by library size for factorFootprints for user defined group samples.
 

 Merge pull request #12 from computational-metabolomics/bug_fix_1_0_1

bug fix issue #7 

 version bump
 

 start adding items to NEWS file
 

 progress bar when generating plots for ZIP download
 

 Merge branch 'RELEASE_3_11'
 

 Fixed colour assignment
 

 Added option to hide non-sig pathways in plot_correlations
 

 bumbed version
 

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 

 version bump
 

 rm importFrom clusterExperiment
 

 Update documentation (R > 4.0.0; Installation from Bioconductor)
 

 Update SangerAlignment reverse read testthat error
 

 Fix sangerRead testthat error
 

 Fix primary seq reverse trimming start & end point error
 

 Fixing secondary peaks (reverse raw data)
 

 Update readme.md 

 updating call for interactive heatmap in the template report
 

 Replacing the archived d3heatmap with heatmaply and plotly - work as drop-in replacement
 

 updated content for pkgdown setup
 

 added badge for GH actions, looks all good on all OSs ;)
 

 trying httr and covr as binary
 

 Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 

 Updated the news - after revision suggestions
 

 Highlighting syntax for R blocks in README
 

 Installing also dependencies in Suggests with extra parameter specified
 

 Added collapsible element to remind to perform proper EDA before testing for DE in Data Setup panel
 

 Added subsection for addressing the point of which version to use, with respect to the user profile.
 

 fixing deps in gh actions
 

 Set and explain dependencies = TRUE in the devel install procedure
 

 Handling alternative normalization/transformation via vst instead of rlog
 

 Replacing d3heatmap, bringing in heatmaply
 

 added badge to README
 

 Merge remote-tracking branch 'upstream/master'
 

 Highlighting syntax for R blocks in README
 

 Updated roxygen version
 

 Linting main function
 

 Linting tests
 

 More linting :)
 

 Linting round, correlatePCs, distro_expr, and genespca
 

 updated to newer roxygen version
 

 bumping version 1.9.1

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION
 

 removing chr name check on peak caller and keepRelevantChrs
 

 Version bump
 

 adding more legend args
 

 manage error message
 

 hotfix to allow download on windows
 

 fixed broken link from biomart with own copy of gene defs
 

 Bump version
 

 Add upper and lower bounds for nlminb of 1e16 to handle extreme cases
 

 Fix potential bug by explicitly calling std::abs() in C++
 

 More leftovers from "1:"
 

 swap red and green in plot
 

 Merge pull request #53 from lgatto/master

fix: deprecate doproduct signature 

 test: add dotproduct deprecation test
 

 chore: bump version number
 

 chore: rerun roxygenise
 

 docs: add note about missing reference implementation as suggested by @jorainer
 

 docs: add 'see details section' for m and n argument
 

 docs: add some newlines as suggested by @jorainer
 

 feat: add navdist
 

 feat: add neuclidean
 

 refactor: remove old dotproduct
 

 feat: add .calibrate
 

 Avoid check on windows as it does not throw an error.
 

 Generalized package listing functionality for environments.
Updated tests that use freezing internals.
 

 Don't bother to deactivate the conda environment.
Removed dry run code from useBasiliskEnv.
 

 Updated DESCRIPTION.
 

 Merge remote-tracking branch 'bioc/master'
 

 Really get quantile information of consensus clusters when requested.

(instead of silently using the tag clusters by mistake)
 

 Fix failures on CAGEexp objects containing a single sample.
 

 Merge branch 'REALEASE_3_11_and_after' into BIOC_master
 

 roxgen2 update.
 

 fixing table bugs and tutorials
 

 Remove all of the bookdown intermediate output.
 

 Transplanted the contents of rebook here for testing purposes.
 

 Merge remote-tracking branch 'upstream/master'
 

 Improved markdown reporting
 

 Update README.md
 

 Add travis badge
 

 Update DESCRIPTION
 

 Update NEWS.md 

 Update DESCRIPTION 

 Provide more clearly warning or error message if the input is not sorted or contain NA values.
 

 Return iterations = 0 instead of NA if dispersion estimate is instant
 

 add getStatistics to export
 

 Update README
 

 Update new GitHub action script from kevinrue

https://github.com/iSEE/iSEE/blob/master/.github/workflows/R-CMD-check.yaml
 

 more work on plotting w numeric x
 

 Update NEWS
 

 Update documentation to latest version (1.1.2) of MatrixGenerics
 

 Add citation
 

 Version bump
 

 showAsCell() now trims strings that are > 22 characters
 

 remove coercion to defunct RangedData
 

 Fixed issue from #4
 

 Fix showAsCell() on ordinary data frames
 

 discrete_legend_body(): adjust ncol and nrow if there are empty rows and columns in the layout.
 

 fixed typo
 

 add instrument in the app
 

 Update README.md 

 change from http to https
 

 add comments
 

 export heatmaps as a shiny app
 

 ht_list is saved into an environment
 

 add selectArea()