version numbering
 

 remove sci notation on file output and update vignette
 

 push codecov support
 

 trigger code coverage
 

 add travis badge
 

 make unit tests correspond to new defaults
 

 add travis support
 

 added vioplot dependency
 

 Remove from daily build report

  - still causing ERRORS
 

 added dataMode to BioMM()
 

 Added entry to vignette for supplying zlib location
 

 More experiments with providing zlib location
 

 readme update
 

 edgeR 3.27.9
- Lengthen author list in DESCRIPTION file to include people who contributed particular functions.
- Update Davis McCarthy's email address in maintainer list.
 

 Update Aaron's email address. Remove emails for authors.
 

 update users guide and help pages.
 

 add gencode v29
 

 X11
 

 11
 

 Merge pull request #301 from csoneson/quickerboot

Quickerboot 

 Merge branch 'master' into quickerboot 

 Merge pull request #300 from csoneson/reboot

File upload from a running iSEE instance 

 typo
 

 further fix tests
 

 rstudio trims whitespaces
 

 Updated whole documentation
 

 test updated
 

 disable coverage for functions that require a shiny session
 

 integer(), character(), and others are given an integer scalar in tests
 

 Added support for file uploads with server re-initialization.
Bugfixes to observers, moved SE setup into server.
 

 Merge branch 'master' of github.com:waldronlab/MultiAssayExperiment
 

 reformat news from REL
 

 minor change
 

 update yml files
 

 minor typo
 

 update code chunks
 

 ignore mutations on edges of chromosomes
fix for #15
 

 include Jeremy new library data structure to speed up alignment
 

 CXX14
 

 fixing vig cliper,DEGraph, SPIA
 

 New global argument for using local cache
 

 Change LOCALHUB to LOCAL to avoid redundency
 

 New global argument for using local cache
 

 rename LOCALHUB as LOCAL

- 'HUB' is redundant
 

 Merge pull request #8 from mjsteinbaugh/master

Fix typo in documentation related to CACHE 

 updated news and description
 

 removed the example using omics2chrlist()
 

 fixed bug with dcPipeline where custom pipelines generated binary matrices
 

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

 18 July 2019: limma 3.41.10

- roast() and mroast() now have the option via a new argument `fast`
  to user an even fast although less accurate approximation when
  converting t-statistics to z-scores.
 

 Update text for bioconductor webpage
 

 pROC imported in the required functions, doc
 

 Use clang for Travis builds on Mac
 

 test on osx as well as linux
 

 version bumP
 

 version bump
 

 update windows build targets
 

 try to fix the strand error in splitGAlignmentsByCut
 

 update travis.yml
 

 Update to V0.99.31
 

 fix carrying over the 'which' names to 'NumericList' return value
 

 proper marker handling
 

 fix vignette headers
 

 add juicebox and hicexplorer capabilities
 

 convert default to more robust
 

 Merge remote-tracking branch 'upstream/master'
 

 update link to github report
 

 homogenise attribut names
 

 modify kmer size of kallisto index when read length is < 50bp
 

 Make more logical functions (#85)

* added uORF function and more docs

* small fix

* fixed spaces
 

 prova
 

 17 July 2019: limma 3.41.9

- roast() and mroast() now perform rotations in chunks to conserve
  memory usage.
 

 Merge pull request #38 from UCLouvain-CBIO/19_Q2

19Q2 

 zzz.R update for 19Q2 metadata
 

 conversion of entrez_id to int
 

 Delete make-metadata.R

Revert to two different make-metadata.R files for each data release 

 metadata info change
 

 19_Q2 changes
 

 Delete metadata.csv 

 Delete make_data.R 

 Merge pull request #34 from tfkillian/master

19Q2 changes 

 metadata.csv
 

 remove metadata section
 

 add rd files
 

 fixing checks...
 

 Merge pull request #30 from tfkillian/master

onLoad function 

 onLoad function
 

 Merge branch 'master' of github.com:UCLouvain-CBIO/depmap
 

 Merge pull request #29 from tfkillian/master

changed repository name 

 Merge pull request #28 from tfkillian/master

EH changes to visualization vignette 

 remove rda data
 

 Merge pull request #27 from tfkillian/master

data import vignette (new EH depmap vignette) 

 Update README.md 

 changes to DESCRIPTION and make-metadata
 

 ExperimentHub metadata changes
 

 DESCRIPTION update to include biocViews
 

 added biocViews: ExperimentHub
 

 Merge pull request #22 from tfkillian/master

experimenthub changes 

 Merge pull request #21 from tfkillian/master

edits to fix errors on build/check 

 Merge pull request #20 from tfkillian/master

removed whitespace .R files and regenerated .Rd files 

 Merge pull request #19 from tfkillian/master

Merged changes to .R and .Rmd files. .Rd files were pulled due to conflicts and will be added in the next commit 

 merged conflicting changes
 

 fixed typo in copyNumber.R
 

 bump version
 

 updated .R, .Rd, visualization vignette and DESCRIPTION
 

 Remove hardcoded root.dir (Never hard-code a path! This makes it non-portable)

Also remove superflous spaces.
 

 fix syntax
 

 add author@R and simplify description
 

 Merge pull request #13 from tfkillian/master

grammatical changes for PDF manual 

 grammatical changes for PDF manual
 

 changes to mutationCalls to remove warning flag
 

 merging
 

 fixed mutationCall issue that was showing a flag on build/check
 

 finished vignettes no issues
 

 merge to fix conflicts
 

 redone data, .R, .Rd files with correct data headers
 

 Delete visualizations.html 

 Delete mutationCalls.rda 

 Delete crispr.rda 

 Delete TPM.rda 

 Delete visualizations.html 

 Delete rnai.rda 

 Delete metadata.rda 

 Delete copyNumber.rda 

 Delete RPPA.rda 

 DESCRIPTION line change
 

 readded correct data files
 

 reupload correct data files
 

 Delete metadata.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 

 Delete copyNumber.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 

 Delete RPPA.rda

need to reload data files because they have the wrong header and github won't update them because the files are too large 

 Merge branch 'master' of github.com:tfkillian/depmap

"trying to resolve data header issue"
 

 Merge branch 'master' into master 

 build check changes
 

 .Rd, DESCRIPTION, README.md and vignette updates
 

 wrap lines
 

 Merge pull request #6 from tfkillian/master

updated long format data .rda .R and make_file 

 vignette update
 

 Merge branch 'master' into master 

 use long format for rnai
 

 red-added vignette and .Rd files
 

 edited R files
 

 start make_data file to replace data cleaning vignette
 

 Merge branch 'master' of https://github.com/tfkillian/depmap into tfkillian-master
 

 Added clean data vignette with cleaned depmap datasets
 

 vignette diagrams
 

 Merge pull request #2 from tfkillian/master

depmap_1.0 

 Graphics
 

 Some changes
 

 updated vignette
 

 I have updated the DESCRIPTION, NAMESPACE, README.md and data.R files and added a CONDUCT file
 

 first version of package
 

 test number issue 2 fixed
 

 RStudio editor options.
 

 store input file
 

 dfd
 

 add CITATION
 

 Update doc
 

 Fix doc
 

 Update CNVRanger.Rmd
 

 vignette_improvement
 

 adding in betabin cpp to examples
 

 cache to false
 

 adding Constantine as contrib, fixing docs
 

 Avoid unnecessary iterations in nOrMoreInCell()

The original function iterated over each sample and thus repeated a lot
of work if the design matrix is simple (eg. two groups).
This is problematic because for large number of samples, this function
takes up a considerable fraction of the runtime of DESeq().
 

 Improve performance of fitDisp()
 

 Comment out printing in fitBeta
 

 version bump
 

 update findMarkers
 

 Merge branch 'master' of github.com:zhewa/celda
 

 add magrittr import
 

 Fixed style issues
 

 Fixed bug in setting the max features to print
 

 Fixed the tree height issues
 

 Merge pull request #191 from zhewa/master

fix topRank doc 

 Merge pull request #187 from zhewa/master

remove redundant clustSplit 

 Style edits
 

 Merge pull request #1 from campbio/master

pulling updated master branch with my fork 

 added json import

requires jsonlite import
 

 Version bump

 

 commented out test unused test code

 

 Removed dependency from a remote file in vignette

 

 Updated docs and namespaces

 

 updated test suite

 

 Added functiopn to get the first non-comment line of a file

 

 Updated bed examples

 

 

Add new test files for toGRanges tests 

 Update plot_utils.R
 

 rename_taxa now use 1st column as key and 2nd column as value
 

 full_join method for phylo object
 

 update release version
 

 remove warning 'implicit list embedding of S4 objects is deprecated' in the graph merging process
 

 c++ win
 

 Multiple testing procedure corrected
 

 16 July 2019: limma 3.41.7

- Improvements to zscoreT() so that `approx=TRUE` works for NA `x`
  values and `approx=FALSE` works for very large or very small `df`
  values. A new simple robust approximation from Wallace (1959) was
  added to handle the latter two cases. Previously `approx=FALSE`
  treated any `df` greater than 10000 as infinite; this threshold is
  now raised to 1e300.
 

 add version bumb to upstream
 

 Removed c++11 references that are making BUILD fail in R3.6.0
 

 changed to bioclite to biocManager in Compatible_Annotation_DBs examples
 

 updated package site
 

 add pROC package for roc() function
 

 bug fix: stat annotation error on matrix functions

 

 Version bump
 

 bug fix: stat annotation error on matrix functions

 

 Merge pull request #6 from btmonier/devel

Annotation bug fix 

 Version bump

 

 Fix count annotation bug

 

 Version bump

 

 Merge branch 'devel'

 

 Update installation info; add download stats

 

 Merge branch 'devel' 

 Update contact information; add biocView tag

 

 Merge branch 'devel'
 

 Initial commit
 

 Initial commit
 

 Merge branch 'master' of github.com:tiagochst/ELMER
 

 Fixing create mae if sample map has same names
 

 remove par from plotMotifStackWithPhylog
 

 Adding correlation argument to get.pair
 

 try
 

 fix the issue for grid.eti default units of plotMotifStackWithPhylog
 

 added \donttest to remove installation error in example
 

 Bump version

1.3.5
 

 Update tests

Improve code coverage
 

 Update README.md 

 Update index.html
 

 Update .Rbuildignore 

 Update README.md

Add codecov badge 

 Update .travis.yml 

 Update index.html
 

 Create .travis.yml 

 Merge branch 'master' of https://github.com/dsrobertson/onlineFDR
 

 Merge pull request #12 from dsrobertson/pkgdown

Add pkgdown site 

 v-1.1.7
 

 Add manual
 

 Bugfix and better checking for valid arguments

    o Bugfix: Added signature( "FixedExpressionData", i=ANY, j=missing ) for the "[" and "[[" functions
    o More indepth checking of function arguments
    o Additional unit tests
 

 changed the way pvalues are being added to the GenoGAM object due to changes in the underlying object from a dependency
 

 updated namespace
 

 bug fix
 

 v-1.1.6
 

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

 Version 0.99.8

Instead of single classifier definition files, the .classifierHook containing all standard classifiers is now merged in the sysdata.rda file.
 

 Version 0.99.6

-the only places where the @ to access slots are used are in getter/setter functions.
-rewrote the class 'initialize' functions as constructors.
-shortened the dataset names
-replaced the datasets by a systemdata.rda file for internal namespace use only
-replaced the checks during package loading by unit tests.
 

 Version 0.99.4

Vignette update
 

 Version 0.99.2

In response to the Bioconductor review many changes were made.

In general:
1) S3 classes were replace by S4 classes. Therefore a complete restructuring was performed resuling in a more modular structure and better maintainable code.
2) More selective importing and exporting in the NAMESPACE file. (Using roxygen2)
3) Adjusted the grammar according to suggest in the review
 

 Version 0.99.0

First commit
 

 update 2019 july
 

 update version  1.10.1

update version 1.10.1
 

 Remove set.seed usage in R code

Remove set.seed usage in R code
 

 fixing errors warning notes

fixing errors warning notes
 

 Merge pull request #2 from lwaldron/patch-1

Correct GitHub links in DESCRIPTION