Recovered wrong C file
 

 vignette updates
 

 version bump
 

 Merge branch 'master' into RELEASE_3_8
 

 Fixed installation instructions and package home line
 

 Fix comparison between pointer and integer (pValue=='\0')
 

 Tidy blocksize error msg
 

 Update 1.3.0
 

 v1.1.2
 

 Minor doc edit
 

 Fixes #26

With Bioc 3.9, there are 4 builders, not 3,
so the html scraping code was broken.
 

 Added new filter "None", set as default
 

 Change to as_tibble
 

 Update vignette to fix bioconductor build error
 

 api change for metadata (removed test 1.3); update email after move to AUG;
 

 bump version
 

 removing large HDF5 file that prevents update
 

 version bumbing
 

 now IndexHopping is Conservative
 

 version++
 

 Removed package reference in links.
Bumped package version, date.
 

 Add Rsubread bioRxiv paper to align, featureCounts and buildindex Rd pages.
 

 consistently use 4-space identation
 

 v1.23.9: fix scaling in if condition in qExportWig

Merge branch 'master' of github.com:fmicompbio/QuasR

Conflicts:
	DESCRIPTION
	R/qExportWig.R
 

 Delete extra space
 

 Use tabular format for Value section. Remove reference.
 

 bug fix for named covariance matrix list
 

 unit test reflects bug fix
 

 version bump
 

 Merge branch 'master' into dosage 

 missed one thing to comment out
 

 updated assocTestAggregate for fastSKAT and fastSMMAT
 

 wip: adding in support for fastSMMAT and rewriting fastSKAT
 

 add option to read dosage from DS field instead of genotypes
 

 added standard runTests() function, prepare for package rewrite
 

 Merge pull request #1 from smgogarten/dosage

add method to read dosage from DS field 

 Fixes #79 in isOutlier (log=TRUE with per-batch thresholds).
Added tests for per-batch threshold reporting.
 

 add travis
 

 update test for spectral matching (too time consuming) (#26)

 

 Removed explicit R dependency from all DESCRIPTIONs.
Bumped date in internal DESCRIPTIONs.
 

 Remove explicit R dependency, Depends on BiocParallel.
 

 Merge branch 'master' of github.com:compbiomed/singleCellTK
 

 Merge branch 'mmkhan19-master'


Former-commit-id: e53ba94e1ec5a296d8923ad7215946639ffd17bd 

 Make theme configurable


Former-commit-id: a41424633acc613ade4371d1aad967f068baf0b2 

 resolved issue #177 - stop reactivity of tabsetpanel in enrichR tab.


Former-commit-id: f21c50f937558891db0d54c35168dcd77ffe6c2c 

 new UI, increased the range of visGenes to 25, restructured visplot code, no condition for barplot, version bump


Former-commit-id: 2a902149c826bb0754230725827366fd0286ea27 

 changed stop() to shinyalert() to maintain consistency for diffexSavedResults(), changed myValues and dList to diffExValues and diffExList respectively and restructured code for saving the results when an alert is encountered


Former-commit-id: 8b1ebf032f37f7986de501f43f6848364f6e28cd 

 help notes in enrichR and diffex tab, fixed the issue in saving diffex results with a unique name, version bump


Former-commit-id: cf2921685aaad58290d6ca735b80279cf8d07da3 

 version bump


Former-commit-id: 9e1f988703133132e5f7f2949f2f29edbad3d07a 

 updated bioconductor packages and resolved the dataframe error, ordered padj columns, removed unncessary code from loadsavedresults(), added  code for exact match of loading similar names of saved results


Former-commit-id: cb11f9d431b7acc2c3913f71fa1822843ba884d3 

 replace 1: by seq_len()
 

 faster scaling function
 

 ready for submission to f1000
 

 bug fixed v1.7.3
 

 fix mismatch in BayesGLMLike prototype vs representation
 

 minor typos 

 corrected emails
changed maintainer email to cp@fgcz.ethz.ch
 

 Fixed remaining (un)signed integer comparison warnings.
 

 Renamed delayed_matrix to delayed_reader for consistency.
 

 Mentioned use of largest niters in emptyDrops.
 

 Discard automatically invalid pathway data files
 

 fix UTF encoding issue (long hyphens)
 

 update ExperimentHub IDs in vignette
 

 version
 

 Add requested SourceType FCS in validation

  - reportedly widely used as the standard filetype for both flow cytometry and mass cytometry
 

 version bump
 

 Fix output of system2 grep call
 

 big fix: adult dup row name and adult inverted fig legend
 

 Update README.md 

 Update brainImageR.Rmd 

 Update README.md 

 add M20
 

 update NEWS
 

 update Bodenmiller_BCR_XL dataset; update description slots in flowSets
 

 clean up
 

 v1.13.2 make that PECA chunk in vignette is not evaluated to prevent build errors
 

 Updated expected platelet cluster for emptyDrops RNG changes.
 

 version bump and date
 

 declare prototype for all slots
 

 Fixed seeding in shuffle tests, extended sanity checks.
 

 Added casts to avoid signed/unsigned comparisons.
 

 Merge branch 'vdsukhov-master'
 

 Update LICENCE 

 description update
 

 Fix wrong slot naming in classes extending AnnotationFilter
 

 Modify perl script to include transcript and gene versions

- Modify the perl script to extract the gene and transcript IDs with version
  from Ensembl (issue #89).
- Add columns tx_id_version and gene_id_version to the transcript and gene
  database tables.
 

 fixed loading of default file in shiny apps
 

 pathway
 

 Bump minimum beachmat version on advice of Aaron
 

 Merge remote-tracking branch 'bioc/master'
 

 Version bump for beachmat update.
 

 Update to the version 1.21.1
 

 Update to the version 1.21.2
 

 use R_NilValue SEXP rather than NULL in Rf_MakeExternalPtr()
 

 fix cluster naming and plots
 

 bump
 

 add test case. #43
 

 bump
 

 revalidate figs for test cases. #43
 

 fix the geom_gate dispatching error. #43
 

 version fix
 

 Merge branch 'RELEASE_3_8' of git.bioconductor.org:packages/debrowser into RELEASE_3_8
 

 Merge branch 'master' into RELEASE_3_8
 

 Merge branch 'master' into RELEASE_3_8
 

 Citation added to the documentation
 

 Some alterations
 

 Change legend title font size for barplot
 

 Change font size for boxplot
 

 Change palette color
 

 version bump for levi's change to vignette
 

 put head() around unique(eh$dataprovider)

The pages of output currently make the vignette look bad (https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html#experimenthub-objects) 

 Streamlined simple LIN output class.
 

 Avoid promiscuous includes, removed extraneous header files.
 

 Define external_ptr class to avoid rule-of-5'ing external_reader classes.
 

 Updated test code for new external API.
 

 Switch external reader API to use pointers to Rcpp classes.
 

 serial execution of the method is now the default
 

 update to README
 

 Hotfix2 jan19 (#67)

* reimplemenation of pmapFromTranscripts in c++

* added the tests

* fixed some docs
 

 Spectral matching rt filter and new match factor algorithm implementation (#24)

* test and print clean up

* added RT and match factor spectral matching approach
 

 version bump 

 use adduct split with metadata (skip when metadata not available)
 

 update citation
 

 bug fixed of theme_tree2(),
see also #218
 

 Changed screen output from simReads()
 

 Change the option name for simReads(): TPM => expression.levels
 

 package name made lowercase
 

 DT table fix while running with runApp("R")
 

 Minor documentation fixes.
 

 Do not build Travis in Windows

It is not supported
 

 Add test with GSC

I don't know how are they loaded
 

 Correct mistake on linking the vignettes
 

 Merge branch 'master' of github.com:llrs/BioCor
 

 Simplifies correctly the gsc (Closes #17 )
 

 Update to make it easier to read
 

 updated markdown preparatory to submission to f1000
 

 Remove check for now-impossible HDF5 seed error.
 

 Bumped version number, date; updated R dependency.
 

 Explicit casting for signed/unsigned comparisons.
 

 fixed Collate field
 

 version bump
 

 bump version number
 

 bump version number
 

 bump version number
 

 bug fix- diffcyt changed 'marker' to 'marker_id' in results
 

 Bug fix: motif_tree() now works with dist objects without throwing an error
 

 devel 1.1.11
 

 changed description formatting
 

 Cleaned up DESCRIPTION, bumped version to trigger rebuild.
 

 initial attempt to manage connections without using the GC
 

 Bug fix: more strangely behaving MotifDb code addressed in Advanced usage vignette
 

 setop dispatch is now S3 => S4
 

 Bugfix to H3K9ac workflow.
 

 uncomment targetFiles <- NULL

otherwise if statement on line 164 fails
 

 update readme
 

 rescale_tree from ggtree
 

 Standardized alignment for NF-YA and H3k4me3 datasets.
 

 Fix to H3K9ac alignment script for better downstream results.
 

 no file output set to default and supression of warning about ties in ks.test
 

 version bump
 

 Create LICENSE 

 Update to the README
 

 small update
 

 small update
 

 resolve merge & bump version
 

 add dplyr::arrange to imports
 

 replace class() with is()
 

 replace re with daf in example
 

 add FlowCytometry to biocViews
 

 fix at the tests
 

 Correct spelling of "Occurrence"
 

 Bump version
 

 Rebuild pkgdown site
 

 Disable participant group tests for non readonly users
 

 Fix for failed test in previous commit.
 

 Pushing data for AssessORF v1.1.5
 

 Removing all data objects
 

 update dotplot
 

 update docs
 

 update author listing
 

 MRCA methods
 

 Merge pull request #16 from heavywatal/fix-rd-width

Remove rd warning by separating the line 

 Remove rd warning by separating the line
 

 version
 

 version
 

 add alias function 'topClusters' for backward compatibility
 

 update docs
 

 update readme
 

 update docs
 

 Speed-up length and gcc
 

 devel 1.1.9
 

 Bumped version number, date.
 

 Avoid promiscuous includes in C++ code.
 

 Added stream option to all calls to PRNG-containing C++ code.
 

 lhei with col.sideColors for CIM()
 

 Bug fix: trying to prevent R CMD BUILD from changing the behaviour of vignette examples using MotifDb
 

 Bug fix: merge_motifs will not show repeat families, organisms, and show method will not show altname as name
 

 Added back the repMask function
 

 update vignette
 

 change readme to .md
 

 add ImmunoOncology to biocviews
 

 bug fix: use 'assay001' name in H5 file, fix list names
 

 minor change: lowercase s in Homo sapiens
 

 update helpers to use EHub, update vignette, and qualify imported functions
 

 wip vignette changes
 

 update curatedTCGAData to support methylation
 

 update fileMatches result from index
 

 update metadata.csv file
 

 update Description in DESCRIPTION
 

 update docs with updated data
 

 support new methylation files in documentation function

- use metadata table as unified object name and location resource
- add helper for accessing parts of metadata table
- use lapply method for loading and obtaining metadata for data resources
- document methylation datasets last
 

 include REPO var if missing
 

 update bits2rd.R script
 

 update makeMetaDocs script
 

 Merge remote-tracking branch 'origin/master'
 

 Merge remote-tracking branch 'upstream/master'
 

 fix the bug in annotatePeakInBatch which can not accept bindingType parameter.
 

 Merge remote-tracking branch 'upstream/master'
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 

 fix global name note
 

 added tests for DelayedMatrix, updated NAMESPACE with roxygen2, adjusted documentation
 

 added filepath as variable to let the user decide where the output file is suppossed to be saved for the delayedmatrix input
 

 added chunk.size as input parameter do how many columns are smoothed simultaniously when using DelayedMatrix as input for the count data
 

 changed r version from release to bioc-devel in travis.yml
 

 Update vignette
 

 Merge remote-tracking branch 'upstream/master'
 

 Bugfixes for the CBP workflow.
 

 update
 

 Update NEWS file
 

 replace 1: by seq_len( in plotVar
 

 replace 1:x by seq_len(x)
 

 add plot.tune.rcc function
 

 comment out cat(results) in tune.rcc
 

 Merge branch 'master' of https://github.com/mixOmicsTeam/mixOmics
 

 Update README.md 

 Update README.md 

 Merge remote-tracking branch 'upstream/master'
 

 Fix description
 

 Removing devtools
 

 add force_build parameter to buildSummarized
update vignette
change tx_db to annotations for multi_de_pairs
update examples
add error checking for sample numbers
 

 update missing dependency
 

 update counts
version bump
 

 Remove :::
 

 remove warning
 

 Exporting functions used in ELMER
 

 Removed old email.
 

 Fix crash when coverage contains no off-target reads, but off-target regions were defined; version bump
 

 don't change working directory on interactive unit tests
 

 add function cleanPeptides
 

 light cosmetic