Merge remote-tracking branch 'upstream/master'
 

 Update package description.
 

 Update code for the 'diffMethod' parameter.
 

 Add baySeq.
 

 Encapsulate call to DESeq2.
 

 Applying changes from 3.11 to master.
 

 replace DMwR with DMwR2
 

 Change version number to 1.5.1
 

 test
 

 Typo fixes to the vignette.
 

 Auto-move Hub caches to their new locations.
 

 Update make-metadata.R
 

 Minor doc update.
 

 Updated test for fixed dqrng seed issue.
 

 Speeding up vignette
 

 Actually try running the path method, to ensure it actually returns.
 

 Replaced sapply() by vapply()
 

 Replaced deprecated survival::survConcordance.fit with survival::concordancefit
 

 update vignette example
 

 Merge branch 'devel_2_1' into master_bioconductor

* devel_2_1: (95 commits)
  updating website
  updates to fix warnings and errors for packaging (bioc submission prep)
  lpSolve shift the negative values to positive space
  add packrat to gitignore
  Bug in inverse Carnival fixed! (was related to character type vs numeric in priorKnowledgeNetwork in Sign column). Multiple tiny style corrections and fixes
  removed visualisation files, setup solvers can do test runs now for each solver, inst folder updated for examples and test runs to work.
  All functions in z_obsolete marked as deprecated. Automatically identified cplex path possibility added (not fully implemented yet).
  All checks fixed. Introduced new API function to run precheck on carnival input
  Presentation
  solvers checks working again. Redundancy fully removed.
  updated api documentations; removed not needed file
  style updated in cplex parse log; corrected solve carnival - correct params list; generalising options checks - all solvers are checked in the same way. Not working code (yet).
  extensive documentation for solve carnival, added examples for basic api. Fixing packaging for which -> match in lp solve code (didn't work with devtools::check())
  updated API for options and default options, API functions with fewer arguments now.
  fixed: bugs in constraints 6 and 7 (several identical constraints were made), global reassignment of constraint 8; bug in constraint 9(when provided same node as measurement and perturbation); bug in measurements backward compatibility (wrong order)
  Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1
  no message
  fixed incorrect constraints generation: constraints 8 and 9; hid global variables (now functions calls), corrected params list in obsolete and new functions
  no message
  no message
  ...

# Conflicts:
#	.gitignore
#	DESCRIPTION
#	NEWS.md
#	docs/404.html
#	docs/articles/CARNIVAL.html
#	docs/articles/index.html
#	docs/authors.html
#	docs/index.html
#	docs/news/index.html
#	docs/pkgdown.css
#	docs/pkgdown.yml
#	docs/reference/index.html
#	docs/reference/runCARNIVAL.html
 

 updates to fix warnings and errors for packaging (bioc submission prep)
 

 add packrat to gitignore
 

 Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1

* 'devel_2_1' of https://github.com/saezlab/CARNIVAL:
  Presentation
 

 Merge pull request #60 from MatteoSpatuzzi/devel_2_1

Add Matteo Presentation 

 All functions in z_obsolete marked as deprecated. Automatically identified cplex path possibility added (not fully implemented yet).
 

 Presentation
 

 updated api documentations; removed not needed file
 

 extensive documentation for solve carnival, added examples for basic api. Fixing packaging for which -> match in lp solve code (didn't work with devtools::check())
 

 Merge branch 'pr/59' into devel_2_1
 

 Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1

# Conflicts:
#	R/solve_carnival.R
 

 fixed incorrect constraints generation: constraints 8 and 9; hid global variables (now functions calls), corrected params list in obsolete and new functions
 

 no message
 

 weighted version of carnival works within new code; fixed bug in creating objective function (wrong variables were used), added time to messages; removed os x from travis (not needed and fails with unclear reason on travis server)
 

 renamed api function to avoid clashes with old API runCarnival -> runVanillaCarnival, updated roxygen, cbc solver recovered runs, R CMD check passes with 2 warnings
 

 style corrections; preparing for packaging; fixing lpSolve for new data rep.
 

 travis update, fixing syntax; constraints style corrected
 

 travis update
 

 correcting tests
 

 passing test 1, separating dummy data creation
 

 tests folder structure/naming unified
 

 Merge branch 'devel_2_1' into Testing_constraints 

 small fixes and updates in the docs, added travis support
 

 Reorganization of the unit tests and new unit tests
 

 First Unit_test for createVariablesForIlpProblem subfunctions
 

 New Unit testing scripts
 

 documentation is partially updated, also for obsolete code; aphaweight removed as a param from everywhere.
 

 updated test for constraint 1.
 

 Adding new unit testing function
 

 fix small bug with old data representation
 

 minor fixes, updating the exporting code to be in line with the previous export results.
 

 moving the code around: old lp file creation went to z_obsolete files. Collapsed short files in one.
 

 collapsing similar constraints in one function, moving old constraint code in one file (keeping it for testing purposes)
 

 further update of constraints and objective function code, adapted for the new internal data representation
 

 constraints 6 and 7 are updated for new internal representation
 

 first ideas of different internal representation of data and variables (for easier constraint generation).
 

 big refactoring on functions params in all parts of the code. Added flexibility on new solvers additions. Removed duplication in exports from all solvers.
 

 small (further) refactoring of constraints
 

 small refactoring of constraints - updating names, partial removing experimental conditions code; implemented inversed carnival flavour in new api; minor fixes after regression tests
 

 cbc solver works in new API
 

 lpSolve is working now in changed API. Minor improvements in lpSolve data preparation for running the solver.
 

 fixing two bugs in the output: one with an extra space appeared in Sign column in weightedSIF results, another is missing S/T in Attributes (both introduced with new API)
 

 Merge branch 'reading-from-lp-file' into changing-api

* reading-from-lp-file:
  implemented a simple version of loading preparsed data and lp files, v.1
  Updates to the vignette and the README files. Removed redundant Mybib2 file.

# Conflicts:
#	R/check_inputs.R
#	R/control_node_identifiers.R
#	R/create_variables_all.R
#	R/run_carnival.R
#	R/solve_carnival.R
#	R/solve_carnival_single.R
#	R/write_lp_file.R
#	R/write_solver_files.R
 

 partial constraints clean up
 

 separating exports of solvers to different folders
 

 fix of error message from cplex (line 64 in example 1 generated LP file was empty if as.data.frame transformation skipped for prior knowledge network)
 

 further prepush clean up
 

 minor formatting changes, control index identifiers - new function, old removed
 

 tiny cleanup
 

 api changes, not working code!
 

 Updates to the vignette and the README files. Removed redundant Mybib2 file.
 

 Merge pull request #46 from saezlab/gabora_cplex_log

adding unit test for parse_cplex_log 

 Merge commit '696d4b4e6fd9160b4035b090005e7dd925c0e56e' into devel_2_1

* commit '696d4b4e6fd9160b4035b090005e7dd925c0e56e':
  fix detection of phases when a convergence table is missing
  - pipe cplex log to a temp file and to stdout - got rid of stringr and used baser - fixes for small case studies
  adding parser for CPLEX log

# Conflicts:
#	R/run_carnival.R
 

 - pipe cplex log to a temp file and to stdout
- got rid of stringr and used baser
- fixes for small case studies
 

 introducing default cplex options and default Carnival cplex option, starting to change parameters checks
 

 add vignette
 

 edgeR 3.33.5
- Remove the "BCV" method in plotMDS.DGEList();
- Update the edgeR User's Guide;
- Update NEWS.Rd;
- Update test files.
 

 Merge branch 'master' into bioc-2021-spring
 

 v2.99.19 in news
 

 Documentation updates and minor issue fixed in IntervalFile.R.
 

 update version
 

 release 2.0.5
 

 Remove outputfile from consensusNet()
 

 Add naPer parameter to consensusNet function
 

 * rewrite vignettes with Rmarkdown
 

 * add consensusNet function
* replace parallel backend with doParallel
 

 initial commit
 

 introduce .wrap_lines() to produce lines wrapped to console width

- intended for messages, etc., seen by the user, e.g., facet_options() error
  that might span multiple lines
- adjusts to getOption("width") and hence to, for example RStudio console
  width
 

 Speeding up examples and vignette
 

 Switch default for 'retain.factor.levels' to 'FALSE'

& add tests!
 

 update to NEWS and version to 1.1.3
 

 generate documentation
 

 Fix character/factor labels in clusterPlot()
 

 bump version
 

 use exact PCA
 

 Bugfix
 

 getData refactor
 

 version bump
 

 a and c as log
 

 resolved merge
 

 version bump
 

 Small fixes of R CMD check, BiocCheck and devtools::check
 

 Merge branch 'master' of https://github.com/saezlab/COSMOS
 

 Merge branch 'master' of github.com:saezlab/cosmosR
 

 fixed transforming sapply into vapply when possible
 

 Merge branch 'master' of github.com:saezlab/cosmosR
 

 Update tutorial.Rmd 

 removed paste from condition signaler
 

 Merge branch 'master' of https://github.com/saezlab/COSMOS

# Conflicts:
#	NEWS.md
 

 Required Change - Updated News.md documentation format
 

 shift installation from vignette to main page 

 remove docs folder - github io page will be fixed later
 

 updated readme and relocated figures to inst folder
 

 fix formatiing of news
 

 updated landing page with pkgdown
 

 Corrected a stupid mistake.
 

 Resuelve el issue #7, agrega progress bar a binGenome
 

 Update version
 

 Add rmarkdown to Suggests 

 Speeding up tests
 

 version bump again...
 

 minor changes
 

 Delete .DS_Store 

 Update README.md
 

 bump
 

 Continue to fix warnings and errors

 

 Bump version
 

 Add PsiNorm wrapper
 

 Bump version to 0.99.8
 

 add displayName to featureModuleTable. Remove stringi
 

 fix plotDimReduceFeature label bug
 

 Remove cache files
 

 update for Bioc 3.13
 

 Cleaning up old base.R. Functions now are split by their role in base-*.R files
 

 Adding wrapper functions to base-wrappers.R
 

 Adding optimizers to base-optim.R
 

 Adding core scripts from epigraHMM (initializer, consensus, and differential peak caller) to base-core.R
 

 Adding scripts with EM loops in base-EM.R
 

 Merge pull request #49 from sanchit-saini/parseURI-fix

.parseUri() fix 

 Remove duplicate code already present in BiocIO
 

 Merge branch 'feature/MouseMethylationBeadChip' of https://github.com/epigen/RnBeads
 

 added a possibilty to use bead coverage in greedycut 

 added implementations of basic normalization methods 

 updated a platform support message in CNV analysis 

 fixed enmix.oob for MMBC 

 added more normalization methods to options 

 first version of the QC module for MMBC 

 first version of the MMBC support 

 Merge pull request #113 from azodichr/splatPop_updates

Alright, I think this is ready to merge 🎉. Thanks for addressing all my comments. There might be some small changes to make later on but let's see if it passes the Bioconductor checks first 🤞🏻. 

 Minor changes to tests to avoid #114
 

 Fix vector argument name in expandParams() docs
 

 fixed merge conflicts
 

 Add missing package prefix
 

 minor bug fix: splatPop batches was not able to take in different effect size distribution parameters for different batches.
 

 Added conditional effect feature
 

 Update batch effect function for splatPop to simulate multiplexing
 

 Bug Fix: Gene outlier factors were being assigned to each individual separately. Fixed by assigning gene outlier factors during splatPopSimulateMeans instead of during splatPopSimulateSC. The outlier factor is now saved in the splatPop key.
 

 Typo 

 Update pkgdown.yaml 

 Merge branch 'master' of github.com:Pasquali-lab/UMI4Cats
 

 mend
 

 add vip_summary chart
 

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

 added css to cls and dwn btn
 

 proving dashboards
 

 Remove unigene support
 

 Merge remote-tracking branch 'upstream/master'
 

 Update README.md

Correct developmental installation 

 Removed vapply from the code
 

 solve warnings and notes
 

 -mUpdated CNVRs computation
 

 Update README.md 

 bump version up
 

 remove test
 

 Testfix, added missing import.
 

 Added a realizeFileBackedMatrix utility for downstream use.
 

 update NEWS
 

 fix
 

 Merge branch 'master' of https://github.com/dtm2451/dittoSeq
 

 fix
 

 added in new annotation functions
 

 added in additional annotation functions
 

 Add multiple ribo file section in vignette
 

 Update README.md 

 Fix breakpoints in baits.
 

 version bump
 

 fixing check and BioC check errors and warnings
 

 doc fix #103: names or suids
 

 bug fix #133: alt to IRkernel
 

 add citation
 

 Resuelve issue #3 comentando el codigo de busqueda del string "NA" en nombres de junturas. Pueden aparecer cromosomas con, por ejemplo, nombres tipo rDNA con lo cual no era un buen metodo para encontrar junturas NA. Ademas, el comportamiento que tenia era de debuguing y solo servia para colgar la ejecucion
 

 update Readme.md
 

 postpone new features to next release
 

 Revisit my previous fix to long standing bug in updateObject() on a factor
 

 Changes to tests and help pages to acccommodate loss of UniGene tables.
 

 Merge branch 'anno_3_13'
 

 Small bugfix in select method for OrthologyDb.
 

 Added Orthology methods to collate field in DESCRIPTION
 

 Added OrthologyDb class
 

 Fixed GENETYPE exclusion for C elegans.
 

 Back out removal of GENETYPE BiMap from Rhesus.
 

 Addded BiMap for gene type table.
 

 Removed UniGene queries and BiMap objects. Swapped much of the existing UniGene stuff to query the new gene type table.
 

 Changes to vignettes and ChipDb builder to accommodate loss of UniGene table.
 

 Merge branch 'anno_3_13'

This branch included all the changes to AnnotationForge required by the following updates
that were made as part of building the annotation packages for the April 2021 Bioconductor 3.13 release:

Removed UniGene table from OrgDb packages
Added Gene type table to OrgDb packages
Created new Orthology.eg.db package to map NCBI Gene IDs between species
 

 More changes to ANNDBPKG-INDEX to accommodate building OrthologyDb package.
 

 Removed organism from DESCRIPTION file for OrthologyDb.
 

 Missed a closing curly brace.
 

 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13
 

 Typo in Orthology package name.
 

 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13
 

 Backing out changes - the Orthology package will be easier if it does not follow the usual paradigm.
 

 Added orthology db to ANNDBPKG-INDEX
 

 Added GENETYPE.Rd file to NCBIORG.DB template.
 

 Changed all dbGetQuery calls that are actually executable statements to dbExecute.
 

 Additional bugfix.
 

 Additional bugfix missed in last commit.
 

 Added appendGenetype function to all the popXXX functions.
 

 Initial changes for the removal of UniGene tables and introduction of gene type tables.
 

 build_check
 

 added sex chromosome segments and changed all snv nomenclature to variants to encompass short indels
 

 updated DESCRIPTION 

 Update DESCRIPTION 

 Merge pull request #17 from Ghoshlab/master

Merge pull request #16 from Ghoshlab/feature-label-output 

 Merge pull request #15 from Ghoshlab/master

Updated vignette 

 Merge pull request #14 from Ghoshlab/master

Merge pull request #13 from Ghoshlab/feature-label-output 

 Merge pull request #12 from Ghoshlab/master

Merge pull request #10 from Ghoshlab/feature-label-output 

 Merge pull request #10 from Ghoshlab/feature-label-output

Merge pull request #9 from Ghoshlab/master 

 updated documentation 

 Merge pull request #7 from Ghoshlab/RELEASE_3_12

Merge pull request #6 from Ghoshlab/master 

 updated vignette 

 updated DESCRIPTION 

 updated description 

 Updates documentation
 

 Updates MarrFilter

Now returns removed feature/samples
 

 Merge changes to Master
 

 cutoff added 

 cutoff added 

 Merge pull request #4 from Ghoshlab/RELEASE_3_12

Update version bump 

 working on new dietary text annotation vignette
 

 Update NEWS, Version bump.
 

 Print available databases when wrong database is selected
 

 remove DS_Store
 

 Fix cytoscapeFreeMemory
 

 Fix cytoscapeFreeMemory
 

 adding line to allow warnings in Travis 

 added build buttons 

 Fix default url
 

 Merge pull request #132 from cytoscape/sandbox

Sandbox 

 wrap up
 

 wrap up
 

 wrap up
 

 Fix image bug
 

 Fix image bug
 

 wrap up
 

 wrap up
 

 implement sandbox