Merge pull request #44 from rformassspectrometry/phili

fix vignettes, refactor chromBackendSpectra 

 fix comment jo on documentation
 

 fix checks
 

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

 whitespaces
 

 remove CNV data
 

 Update README.md 

 update before new manuscript
 

 Update README.md

Better readme 

 Fix issue with Standardize_Subset where something inexplicable was happening.

Not sure what I was even intending to do. Previous state of this system was doing
something crazy when passed input of `Subset` that was an integer vector.

I've simplified this codepath to make it more understandable and left some
documentation. Should be working correctly now.
 

 fix test case errors
 

 Justify code extraDistr
 

 With all negative hypergeometric functions in house
 

 Correct version bump
 

 Small Fix, added Rdata
 

 Fix metabolites imported form csv
 

 Added MSnbase to suggests
 

 try adding write permissions into workflow
 

 version bump
 

 version bump
 

 fix: save_QC_plots() default color option
 

 some spaces in a vignette
 

 Merge pull request #58 from drighelli/light_fix

readME and vignette devel installation code line 

 Remove installation section from Protein tutorial vignette

Removed the installation instructions for the SpaceTrooper package from the vignette. 

 fixing interop vignette name in readme and vign
 

 Merge branch 'devel' into documentation_jan25 

 Merge pull request #56 from drighelli/light_fix

Minor fixes to devel code, README and other files 

 fixing details in spatialpercellqc and readandaddpolygons
 

 adding new doc files
 

 fixing doc for readMerfish regarding parameters, adding details
 

 fixing readcosmx doc, adding keeppols arg
 

 version 1.1.3 bump
 

 fixing verbose messages in QC functions
 

 incremented version and added some more description
 

 Modify assay control (#22)

* Allow overwrite of assay when using multiple assays (without warning)

* Remove line left over from MetaboSet-support

* Bump version 

 fix malformatted DESCRIPTION file
 

 init fix
 

 function def
 

 std, isleftgreat fix
 

 Add bioRxiv citation.
 

 Add sticker for smartid.
 

 update bioc check yaml.
 

 Update README.
 

 Version bump.
 

 updating to be sure that 1.0.2 EBI GWAScat version is used, that includes ontology tags
 

 update docs
 

 1.7.2
 

 update docs
 

 1.6.1
 

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 

 1.5.1
 

 1.4.1
 

 1.4.1
 

 update docs and deps
 

 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
 

 update docs
 

 1.3.3
 

 stash
 

 clean up
 

 update figure
 

 update cutoff
 

 1.1.22
 

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 1.1.19
 

 update docs
 

 1.1.17
 

 1.0.1
 

 update news
 

 fix PC scaling
 

 fix bug in checks
 

 1.1.16
 

 1.1.16
 

 update deps
 

 tmp push
 

 bug fix
 

 update
 

 update
 

 update
 

 add outliers code
 

 bug fix
 

 1.1.13
 

 1.1.13
 

 bug fix
 

 add computeVIF
 

 update docs
 

 update docs
 

 1.1.11
 

 add compositePosteriorTest
 

 1.1.10
 

 update vp dependency
 

 bug fix
 

 1.1.8
 

 bug fix
 

 Add checks
 

 update pbWeights tau
 

 update pbWeights tau
 

 bug fix
 

 1.1.5
 

 update pbWeights
 

 1.1.3
 

 1.1.3
 

 stash
 

 1.1.1
 

 update docs
 

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
 

 trimWeightOutliers
 

 0.99.32
 

 0.99.32
 

 update docs
 

 weights
 

 test
 

 reweight
 

 update
 

 0.99.30
 

 clean up
 

 0.99.28
 

 update plotVoom()
 

 0.99.26
 

 0.99.24
 

 0.99.23
 

 update docs
 

 update docs
 

 update
 

 0.99.19
 

 0.99.18
 

 update
 

 0.99.17
 

 update site
 

 0.99.15
 

 Merge pull request #10 from GabrielHoffman/master

0.99.14 

 Merge pull request #9 from GabrielHoffman/master

Master 

 fix typo
 

 fix deps
 

 0.99.13
 

 update
 

 stash
 

 0.99.8
 

 0.99.7
 

 0.99.6
 

 0.99.4
 

 0.99.2
 

 add CITATION
 

 0.99.1
 

 Merge branch 'master' of https://github.com/GabrielHoffman/drealmet
 

 Merge pull request #2 from hoondy/master

Addition of aggregateVar function 

 update docs
 

 fix news
 

 0.0.63
 

 update README image
 

 update metdata
 

 update docs
 

 0.0.62
 

 Addition of aggregateVar function
 

 Create aggregateVar.R

Aggregation function for single-cell log-normalized counts to calculate per-sample variance for dreamlet 

 update docs
 

 update plotForest
 

 Add outlier()
 

 update
 

 bug fix
 

 0.0.60
 

 update
 

 0.0.58
 

 update
 

 0.0.55
 

 0.0.54
 

 0.0.52
 

 update
 

 0.0.51
 

 Update plotGeneHeatmap.R

Helps to retain the original order of genes 

 0.0.50
 

 update docs
 

 update readme
 

 0.0.48
 

 0.0.48
 

 0.0.47
 

 update
 

 stash
 

 update docs
 

 update plots
 

 update
 

 0.0.43
 

 bug fix
 

 add dropRedundantTerms
 

 add dropRedundantTerms
 

 update docs
 

 update plots order
 

 update plots
 

 update facet order
 

 0.0.41
 

 update
 

 update
 

 update
 

 v0.0.40
 

 update dependenies
 

 0.0.39
 

 update diagram
 

 0.0.38
 

 update
 

 update docs
 

 update dependency
 

 update html
 

 fix typo
 

 fix typo
 

 0.0.36
 

 0.0.35
 

 update docs
 

 update docs
 

 update docs
 

 update logo
 

 update 0.0.33
 

 update 0.0.33
 

 update messages
 

 0.0.32
 

 0.0.32
 

 stash
 

 test
 

 update colsum_fast
 

 update colsum_fast
 

 update 0.0.31
 

 update 0.0.31
 

 update 0.0.31
 

 update dependency
 

 0.0.30
 

 0.0.29
 

 update docs
 

 update docs
 

 update docs
 

 update
 

 update
 

 update
 

 update
 

 0.0.27
 

 0.0.26
 

 fix bug in dreamletCompareClusters
 

 Test
 

 bug fix
 

 0.0.24
 

 0.0.23
 

 update progress bar
 

 update docs
 

 bug fix
 

 0.0.21
 

 0.0.21
 

 0.0.20
 

 test
 

 test
 

 test
 

 0.0.19
 

 fix bug in pllotting
 

 0.0.18
 

 0.0.17
 

 bug fix
 

 bug fix
 

 update to filtering