Habil: Version 1.23.4
 

 version bump 1.25.3
 

 version bump 1.25.2
 

 include names with single bracket replacement
 

 use jammy to conincide with devel image
 

 update examples
 

 roxygenize new version
 

 updated readme status badges
 

 [U] Added bonferroni correction in gene_frequency_fisher
 

 [minor] Removed github actions from branch, fixed codecov file and README
 

 Solve chk library deprecations. (#14)

 

 Remove R_front script.
 

 Fixex warning in cellCounts
 

 vignette error
 

 validity vignette man [ackage
 

 importFrom_internal_BiocStyle_dataLoad_pckgLinks
 

 version update
 

 DESCRIPTION updated
 

 MatchedAssayExperiment
 

 readme added
 

 try to fix edgeR error
 

 bump version number
 

 Fix some minor bugs while testing locally
 

 Try using fetch_data() for type = "spatialDLPFC_Visium"
 

 Fixed testing
 

 Fixed error in creating reassignment matrix in the atena method
 

 Version bump.
 

 remove unused files
 

 Merge branch 'master' into selfInteractionRatio 

 change tests values
 

 handles error on tests (pb of data.table agregation format, needs to be all numeric)
 

 correct roxygen
 

 add missing arguments in function
 

 keep zero lines
 

 remove varif if NA values on the median (not allowed), already fixed before KR normalization.
 

 revert compartment assignement. Lower should be A. correct tests. rerun example data
 

 use median of others values if no value on diagonal
 

 coorect test after add of +1 in positions
 

 Correct Windows bug.
 

 removing the +1 in log(+1) in normdistance (after KR = no need). returning results in log to have a nice viz scale (around 0)
 

 reverse compartments attribution (same as before, to compare results)
 

 valids assays must have a non zero variance
 

 correct in case of only 1 column matrix
 

 take only diagonal to detectcompartments, change A to higher values
 

 bump to 1.1.6
 

 GHA update
 

 GHA update
 

 Changed link to TFBS files
 

 refactor: adapt to Sebastian's comments
 

 refactor: use S4Vectors::findMatches instead of grr::matches
 

 ci: use R devel and BioC 3.17
 

 refactor: import spectra<- from ProtGenerics
 

 Updated installation instructions.
 

 Added RANN import
 

 Fixed "jitter" typo in documentation.
 

 Added changes to address issues for Bioconductor review
 

 Update convertData.R 

 Update propeller.anova.R 

 Update normCounts.R 

 Update convertData.R 

 Update propeller.anova.R 

 Update propeller.anova.R 

 Update normCounts.R 

 Update getTransformedProps.R 

 Update estimateBetaParam.R 

 include packages for unit test
 

 Update DESCRIPTION

Add LazyData: TRUE 

 Update README.md 

 Compute NumSig and SetSize like at https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/check_clinical_gene_sets.R since it's useful info to have
 

 Hack to resolve #175 and satijalab/seurat#6489
 

 dis able boost thread
 

 attempt to fix stat_ell
 

 Honeypot template
 

 Didn't run document() to update melt_list_left example.
 

 Add `parallel` argument to `summary` and `lrTest`.
Fixes #169
 

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
 

 ebayes also needs to follow exprs_values
 

 Fixes #158
 

 Fix typo in vignette name. closes #150 

 add .hic and .hicpro files
 

 bug fix - chain file with offline run
 

 Add code for processing Lohoff, et al seqFISH data
 

 Add mouse gastrulation seqFISH data
 

 Addition of seqFISH mouse gastrulation data
 

 README update
 

 Documentation updates
 

 update hpar package man page
 

 udpate metadata (remove .rda extension)
 

 udpate code base to use EH
 

 use roxygen
 

 update title names (omit extension)
 

 feat: update package to use ExperimentHub
 

 fix conflict
 

 fix gha deploy
 

 Merge branch 'ManonMartin-master'
 

 fix: rename object in rnaGeneTissue21.0.rda
 

 Update check-bioc.yml 

 bump to 0.99.6
 

 Update check-bioc.yml
 

 add partial_bundle in plotMetric
 

 use NEWS.md in markdown format
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Version bump devel
 

 29 Nov 2022: limma 3.55.1

- eBayes() now checks whether `fit` is a list object before
  undertaking other tests.

- Update limma-Tests.Rout.save for Bioc 3.16 annotation packages.
 

 bumping version to 2.15.1
 

 comentando el código nuevo
 

 fixing correct Y coordinate in pathway layout in plotVG
 

 updating devel.R
 

 fixing bugs, adding DAsummary pathways_summary functions
 

 adding devel.R file
 

 meta.export
 

 add add_meta() function
 

 Use sparse martix for excluded cells.
 

 bump version number
 

 update URL
 

 bump version number
 

 passing check, using current 'vep' utility instead of a .pl program to use the API
the README mention of Windows may need attention
 

 bump to 1.17.1
 

 update
 

 version bump
 

 update gh page title
 

 Minor wording changes.
 

 update overview vignette, bib
 

 Merge branch 'master' into RELEASE_3_16
 

 0.99.6
 

 New suggestionss welcome!
 

 Fix ecxluderanges typo
 

 Additional git config --global --add safe.directory /__w/excluderanges/excluderanges
 

 Use cont: "bioconductor/bioconductor_docker:RELEASE_3_16"
 

 re-knit
 

 Install pkgdown from cran
 

 Supported report of excluded cells.
 

 regular maintenance
 

 Removed old email
 

 All files now portable
 

 Fixed notes
 

 Adding globals
 

 Added .Rbuildignore
 

 fixed which bug
 

 Merge branch 'devel'
 

 minor doc clarification
 

 fixed sample reporting in fixed mode #66 

 Merge pull request #65 from xnnba1984/master

Import default hyperparams from Xi and Vasilopoulos 

 Update scDblFinder.R 

 minor formatting changes
 

 - Random forest's survival mode now calculates risk values by multiplying sum of survival probabilities by negative one.
- performancePlot and samplesMetricMap now use a variable named metric to consistently refer to the metric.
- samplesMetricMap now has default value of auto for metric. Also, the metric will be calculated rather then stopping with an error, if the metric hasn't been calculated previously using calcCVperformance.
- samplesMetricMap default metric is accuracy, to be consistent with performancePlot.
 

 add HiCool log file
 

 Changing maintainer
 

 Fixed control probes
 

 Merged conflict
 

 Added

From: Jean-Philippe Fortin <jpfortin@ceb-213bl-002.pmacs.upenn.edu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@121682 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Initiating travis

From: jfortin <jfortin@jhsph.edu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@121680 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Added

From: Jean-Philippe Fortin <jpfortin@ceb-213bl-002.pmacs.upenn.edu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@121678 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Warnings as errors
 

 Initiating traviws
 

 Merge branch 'master' of github.com:Jfortin1/shinyMethyl
 

 Initiating travis
 

 Warnings as errors
 

 Initiating traviws
 

 New version with EPIC

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@119994 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Added EPIC stuff

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@119992 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 New version with EPIC
 

 Added EPIC stuff 

 Version bump to trigger package rebuilding now that purl()'ing issue
has been correctly identified. knitr does not create purl()'ed
(Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which
the build system was setting. Now it's not set, so these .R files are
now created. See https://github.com/yihui/knitr/issues/1212 for more.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@117512 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 bump version after creating 3.3 branch


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Bumped version number of all packages after creation of 3.2 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Bump versions in trunk after creation of 3.1 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
 

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Commit id: 8452695664a8f59b9afc265cc8f783897f21caf6

    Update .travis.yml



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    Update README.md



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    Added travis file



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Commit id: e4b320d9027604813041cfe7b86b674e1e8e4201

    Updated citation

Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2015-01-26 21:01:33 -0500
Author date: 2015-01-26 21:01:33 -0500


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    Updated citation

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Author Name: Jean-Philippe Fortin
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Author date: 2015-01-26 15:58:52 -0500


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    Changed test data

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Author Name: jfortin
Commit date: 2015-01-05 15:00:56 -0500
Author date: 2015-01-05 15:00:56 -0500


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 Bumping versions after creating 3.0 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
 

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Commit message: Added paper link
Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2014-08-28 14:10:02 -0400
Author date: 2014-08-28 14:10:02 -0400



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Commit message: Update README.md
Committed by: Jean-Philippe Fortin
Author Name: Jean-Philippe Fortin
Commit date: 2014-07-24 10:37:25 -0400
Author date: 2014-07-24 10:37:25 -0400



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Commit message: Update README.md
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 Adds oposSOM/ pepStat/ Polyfit/ pRolocGUI/ Pviz/ shinyMethyl/ to the repos.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@92064 bc3139a8-67e5-0310-9ffc-ced21a209358
 

 Merge branch 'master' of https://github.com/bcm-uga/LEA
 

 back to sylvester
 

 rename
 

 version UP

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

# Conflicts:
#	.Rbuildignore
 

 delete html
 

 fix test
 

 rbuild ignore
 

 Merge branch 'master' of github.com:stemangiola/sccomp
 

 verison UP 

 add c++
 

 pull from BIOCONDUCTOR dev

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

# Conflicts:
#	DESCRIPTION
 

 Merge pull request #71 from stemangiola/master

rebase 

 Merge pull request #70 from stemangiola/fix-random-effect-with-intercept

Fix random effect with intercept 

 comment
 

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

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

 rm scale_x_logicle from vignette because it is broken in ggplot
 

 Update build.yml 

 Merge pull request #133 from jonathangriffiths/ensembl-chain

Allow use of Ensembl chain 

 version bump
 

 Code changes for Ensembl chain
 

 Merge branch 'master' into jomain
 

 Merge branch 'master' into jomain
 

 feat: add chunkapply (issue #249)

- Add function `chunkapply` and add parameter `chunkSize` to `spectrapply` to
  enable chunk-wise processing.
 

 - performancePlot no longer ignores orderingList.
- Default random forest function now seamlessly works when outcome is a Surv object so classifier doesn't need to be changed from default setting if input data is survival.
 

 remove Sint from C++ code
 

 change to 2 workers
 

 ignore compiled binaries
 

 fix test
 

 rbuild ignore
 

 Merge branch 'master' of github.com:stemangiola/sccomp
 

 verison UP 

 add c++
 

 pull from BIOCONDUCTOR dev

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

# Conflicts:
#	DESCRIPTION
 

 Merge pull request #71 from stemangiola/master

rebase 

 detlete html
 

 add figures scripts
 

 Update README.md 

 allow PCA with uncertainty outputting the draws
 

 Update DESCRIPTION 

 dummy


Former-commit-id: 973e89a04cb7d2aaa5aa451fdfdb2b7d3a2266d4 

 remove sccomp.so


Former-commit-id: b24618ab9535d582595ba082183bbda481f44357 

 include sccomp.so


Former-commit-id: 7264bb969ffe370aa413cda9c12c4e27bfa149b2 

 Merge branch 'random-continous-slope' of github.com:stemangiola/sccomp into random-continous-slope
 

 fix contrasts for missing names
 

 make random effects able with contrasts
 

 Update check-bioc.yml 

 fixes for normal models
 

 allow to create intercept for generate data for intercept-free models
 

 Merge branch 'master' into random-continous-slope 

 fix contrasts
 

 fix contrasts
 

 avoid check
 

 fix
 

 fix tests
 

 restructure random intercept/slope table and allow for continuous random covariate
 

 fix tests
 

 typo
 

 pull upstream

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

Conflicts:
	DESCRIPTION
 

 small fix
 

 fix replicate data
 

 fixed replicate_data for multilevel model
 

 fix for unilevel model
 

 fix miltilevel multiple
 

 expanded multilevel to multiple
 

 rebase

Merge branch 'random-intercept' into remove-unwanted-variation

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 

 Merge branch 'random-intercept' of github.com:stemangiola/sccomp into random-intercept
 

 Update README.Rmd 

 second implementation based on residuals