NEWS

---

easyRNASeq 2.41.1

• Ported changes from 2.40.1

easyRNASeq 2.40.1

• Fixed broken dependencies (Biostrings::type is now BiocGenerics::type and BiocGenerics::clusterApply is now parallel::clusterApply).
• Adapted to changes for Roxygen
• Changed from using biomaRt::useMart to biomaRt::useEnsembl

easyRNASeq 2.27.1

• DESeq dependency removal
• Added extra warning about RPKM usage
• Removed Defunct functions

easyRNASeq 2.26.0

• Bioconductor release 3.12

easyRNASeq 2.25.1

• Ported changes from 2.24.1

easyRNASeq 2.24.1

• Final documentation fix and removal of defunct RangedData unit tests.

easyRNASeq 2.24.0

• Bioc release 3.11

easyRNASeq 2.23.4

• Ported changed from 2.22.5

easyRNASeq 2.23.3

• Ported changed from 2.22.3 & 4

easyRNASeq 2.23.2

• Ported changed from 2.22.2

easyRNASeq 2.23.1

• Ported changed from 2.22.1

easyRNASeq 2.22.5

• Moved the vignette data from the FTP to Git

easyRNASeq 2.22.4

• Moved the vignette data retrieval to the biocFileCache

easyRNASeq 2.22.3

• Ensured that misformatted gff3 prefix containing extra white space characters are gracefully handled.

easyRNASeq 2.22.2

• Fixed a namespace issue
• Extended the cleanup step of the vignette

easyRNASeq 2.22.1

• Added missing steps to the vignette
• Corrected the RobinsonDelhomme2014 metadata
• Fixed a bug introduced by a dropped functionality in asMates
• Updated package version dependencies

easyRNASeq 2.19.6

• More fiddling with documentation link warnings on windows

easyRNASeq 2.19.5

• Fixed more documentation link warnings on windows

easyRNASeq 2.19.4

• Fixed link warnings on windows

easyRNASeq 2.19.3

• Changed to use BiocFileCache for the tests and examples

easyRNASeq 2.19.2

• Added the volume and page in the citation
• Added the ImmunoOncology field per request from Bioc core
• Fixed the documentation warnings on Windows

easyRNASeq 2.19.1

• Dropped the RangedData support as these are now deprecated.

easyRNASeq 2.18.4

• Changed from curl_download to download.file
• Bioc core changes

easyRNASeq 2.18.2

• Added the ImmunoOncology field per request from Bioc core
• Added the volume and page in the citation
• Fixed the documentation warnings on Windows

easyRNASeq 2.18.1

• Adapted an example as RangedData objects are being deprecated.

easyRNASeq 2.15.5

• Ensured that counting happens in a strand specific way when stranded data is provided
• The easyRNASeq and all related methods are now defunct.
• Added a BamParam strandProtocol argument value to count reads on the reverse strand
• Removed calls to RangedData constructor defunct parameters in unit tests
• Removed dependencies to RnaSeqTutorial in unit tests
• Removed the easyRNASeq vignette. Replaced it with a knitr vignette - to be completed.

easyRNASeq 2.15.4

• Removed dependencies to RnaSeqTutorial
• Removed calls to RangedData constructor defunct parameters

easyRNASeq 2.7.7

• Ported version 2.6.3 changes

easyRNASeq 2.7.6

• Ported version 2.6.2 changes

easyRNASeq 2.7.5

• Changes by Bioc Core Dev

easyRNASeq 2.7.4

• Changes by Bioc Core Dev

easyRNASeq 2.7.3

• Changes by Bioc Core Dev

easyRNASeq 2.7.2

• Ported version 2.6.1 changes

easyRNASeq 2.7.1

• Changes by Hervé to update the NAMESPACE

easyRNASeq 2.7.0

• Original Bioconductor version 3.2

easyRNASeq 2.6.3

• Updated the maintainer address

easyRNASeq 2.6.2

• Fixed issues with the gff3 synthetic transcript generation. Several mRNA lines per mRNA were kept and the feature selection was failing for features other than mRNA (e.g. tRNA or miRNA)
• Extended the SimpleRNASeq vignette

easyRNASeq 2.6.1

• Upgraded the dependencies
• Introduced the new vignette (SimpleRNASeq) structure
• Fixed a cosmetic issue
• Corrected man pages
• Fixed issues with the synthetic transcript generation from gtf file. Thanks to Sylvain Foisy for reporting this one.

easyRNASeq 2.6.0

• Original Bioconductor version 3.2

easyRNASeq 2.5.6

• Ported changes from version 2.4.5 - 2.4.7
• Added a function to create the synthetic transcripts
• Deprecated functions fetchAnnotation and knowOrganisms are now defunct
• Export 'basename', 'seqlevels', 'seqlevels<-' and 'seqnames<-'

easyRNASeq 2.5.5

• Ported changed from release version 2.4.4

easyRNASeq 2.5.4

• Ported changed from release version 2.4.3

easyRNASeq 2.5.3

• Ported changed from release version 2.4.1
• Adapted to the genomeIntervals API changes (change from seq_name to seqnames and addition of the coercion methods to GRanges and consort).

easyRNASeq 2.5.2

• Bioc. API changes

easyRNASeq 2.5.1

• Bioc. API changes

easyRNASeq 2.5.0

• Bioc. Devel Version 3.2

easyRNASeq 2.4.7

• Export the SummarizedExperiment accessors: 'colData', 'exptData', 'rowRanges' and 'seqinfo'
• Fixed an issue with Ensembl gtf file parsing reported by Elie Antoun.
• Implemented a minimal sanity check to ensure that at least one genomic reference is shared between the BAM and the annotation

easyRNASeq 2.4.6

• Corrected a bug when asserting strandedness. Monotypic situations (all stranded or all unstranded) were not handled properly. Another catch by Michael Dondrup. Thanks again!

easyRNASeq 2.4.5

• Corrected a wrong signature for the AnnotParam constructor.
• Fixed the AnnotParam print method.

easyRNASeq 2.4.4

• A GRanges API change has been identified and patched by Michael Dondrup. Thanks!

easyRNASeq 2.4.3

• Removed an unnecessary IRanges import (aggregate), which has been merged with the stats package one.

easyRNASeq 2.4.2

• Removed a re-defined fileName generic overwriting a BiocGeneric one that broke the build on SnowLeopard

easyRNASeq 2.4.1

• Uses rowRanges instead of rowData
• Fixed issues in the deprecated gene+geneModel counting approach of the easyRNASeq function.
• Updated the package dependencies
• Adapted the demultiplex function to handle multicore. It is using the Shortread srdistance function under the hood, who internally uses bplapply, without ever detailing so (?!). As a consequence, it would spawn as many jobs as cores are detected and this breaks the vignette processing during R CMD check... As a consequence demultiplex got an mc.cores=1L new arguments that preserve its former serial approach but enables parallel processing, controlled by the user (as it should be!! and not invisibly in the code!)
• Removed the dependency on locfit (importing what is necessary)
• Exporting more functions, mostly locfit and DESeq functions
• Adapted the parameters for the DESeq dispersion plot

easyRNASeq 2.4.0

• Bioc. Release Version 3.1

easyRNASeq 2.3.4

• Bioc. API changes: added missing imports, removed unneeded imports, added a missing package dependency
• Removed generics now defined in BiocGenerics

easyRNASeq 2.3.3

• Bioc. API changes

easyRNASeq 2.3.2

• Bioc. API changes

easyRNASeq 2.3.1

• Same as release 2.2.1

easyRNASeq 2.3.0

• Bioconductor devel 3.1

easyRNASeq 2.2.1

• Added (now) missing S4Vectors function imports.

easyRNASeq 2.2.0

• Bioconductor release 3.0

easyRNASeq 2.1.15

• Removed an apparently unnecessary require call.

easyRNASeq 2.1.14

• Fixed a missing documentation link and a missing object documentation as well as the move of two objects' (DataFrame, SimpleList) generic from IRanges to S4Vectors

easyRNASeq 2.1.13

• Bioconductor Core Team changes to underlying packages

easyRNASeq 2.1.12

• Bioconductor Core Team changes to underlying packages

easyRNASeq 2.1.11

• Fixed more IRanges -> S4Vectors import changes.
• Relaxed the BAM header validation of the SO field. Thanks to John (Zang Jianhua) for finding the issue and providing the fix. Same changes as in release 2.0.9.

easyRNASeq 2.1.10

• Bioconductor core changes Iranges -> S4Vectors

easyRNASeq 2.1.9

• Ported changes from version 2.0.7

easyRNASeq 2.1.8

• Ported changes from the release version 2.0.5 and 2.0.6

easyRNASeq 2.1.7

• Changed to use roxygen 4.0.0
• Corrected a dependency mismatch. Beats me why it did not work in v2.1.6...

easyRNASeq 2.1.6

• Corrected a dependency mismatch.

easyRNASeq 2.1.5

• Same changes as 2.0.3 and adapted dependencies from IRanges to S4Vectors

easyRNASeq 2.1.4

• Some haphazard modification from Bioc.

easyRNASeq 2.1.3

• Same changes as 2.0.2

easyRNASeq 2.1.2

• Completed the previous commit

easyRNASeq 2.1.1

• Same changes as 2.0.1

easyRNASeq 2.1.0

• None, Bioc new devel branch

easyRNASeq 2.0.7

• Made the verbose argument behave as it should
• Updated/corrected some man pages
• Added names to the assays SimpleList

easyRNASeq 2.0.6

• Export the GenomicRanges SummarizedExperiment class, its constructor and its assay accessor method
• Reduced the memory requirement of the annotation GRanges
• Added some redirect to avoid some unneccessary output

easyRNASeq 2.0.5

• Corrected the handling of gtf files to ensure that exons are correctly identified. This required some low level functionality changes. A unit test was added to ensure consistency. "exon_number" is no more a required gtf field, but "exon_id" is.
• Changed the BamFile validation as now the index has the correct .bai extension automatically added in RSamtools.
• Fixed a bug that hardcoded the transcript summarization when using simpleRNASeq.

easyRNASeq 2.0.4

• Corrected a data package suggested dependency version as data package now follow the same versioning scheme as software packages.

easyRNASeq 2.0.3

• Ensured package version consistency - had a Bioc 2.14 and 3.0 mix when checkin 2.0.2.

easyRNASeq 2.0.2

• Added the minimal set of exports for the vignette to be built.
• Fixed some vignette discrepancy with the BiocStyle style.

easyRNASeq 2.0.1

• Moved the vignette from 1.8.8 to 2.0.1; it was overlooked in the 1.99.3 version.
• Corrected the dependencies to be Bioc 2.14

easyRNASeq 2.0.0

• None, Bioc release 2.14

easyRNASeq 1.99.3

• Replicated the bug fixing of version 1.8.8.

easyRNASeq 1.99.2

• Added missing imports

easyRNASeq 1.99.1

• Fixed a bug in the getBamFileList function that prevented reporting accurate error/warning messages.
• Updated the package dependencies.

easyRNASeq 1.99.0

• Ported the final changes from the Git repository that make the simpleRNASeq function functional.
• Bumped the version number to 1.99 as these are major changes and hence next Bioc release will have easyRNASeq 2.0.0.

easyRNASeq 1.9.7

• Same as release 1.8.7 change.

easyRNASeq 1.9.6

• Ported changes from the Git repository including further class refinements and unit testing.

easyRNASeq 1.9.5

• Automatic version number bump by Bioc

easyRNASeq 1.9.4

• Mirrored changes in version 1.8.6

easyRNASeq 1.9.3

• Mirrored changes in version 1.8.5

easyRNASeq 1.9.2

• Ported version 1.8.4 changes to the development version
• Started to import new classes from the git repository as part of the package main function re-implementation

easyRNASeq 1.9.1

• Change from Bioc to insert GenomicAlignments

easyRNASeq 1.9.0

• No changes, new development version

easyRNASeq 1.8.8

• Corrected a typo in a function to get the names from a RangedData annotation. Thanks to Sylvain Foisy for reporting it and providing feedback to squash it.

easyRNASeq 1.8.7

• Fixed a bug in the summarization when using the "genes", "geneModels" paradigm and annotation in the older RangedData format. Thanks to Kelly Stanton for reporting it and providing data to squash it.

easyRNASeq 1.8.6

• Fixed an issue where RPKM values were all set to NAs. Thanks to Vijaya Mahalingam Shanmugiah for reporting that issue.
• Fixed a number of warnings introduced by changes to the underlying IRanges package.

easyRNASeq 1.8.5

• Added a check for handling cases where BAM files do not report the number of alignments through the NH tag. Thanks to Alistair Chalk for spotting that one.

easyRNASeq 1.8.4

• Added a check to filter bai file from the files gathered by the pattern argument.
• Added a check for multi-mapping reads.
• Added a deprecation warning for count='genes', summarization='geneModels'.
• Extended the vignette, with details on the annotation warnings and how to resolve them. Added an FAQ section.
• Modified the annotation warning, redirecting to the new vignette section on how to resolve these.
• Switched to BiocStyle for the vignette.

easyRNASeq 1.8.3

BUG FIXES

• Changed one argument name of the fetchAnnotation function to avoid arguments colliding when providing additional arguments to be passed to DESeq through the ... argument. The argument has been renamed from 'method' to 'annotationMethod'.

easyRNASeq 1.8.2

• Reworked the parsing of gtf formatted files.
• Added a few more sanity checks in the easyRNASeq function.
• Added a use case to the vignette to show how to generate and use synthetic transcripts rather than "gene models".
• Corrected a bug when exporting a SummarizedExperiment for "transcrips" and "geneModels" count methods.

easyRNASeq 1.8.1

• Imported changes that were lost from version 1.6.4
• Adapted the dependencies version to match the Bioconductor release version 2.13
• Switched to use GAlignments instead of GappedAlignments
• Corrected 2 Notes occuring during R CMD check that had to do with the DESCRIPTION Depends and Enhances fields and the use of pkg:::name vs. pkg::name
• Added Bastian Schiffthaler as an author

easyRNASeq 1.8.0

• No changes, Bioconductor release version 2.13

easyRNASeq 1.7.0

• No changes, Bioconductor development version 2.13

easyRNASeq 1.6.4

• Made the plotDispLSD function visible (now proporly exported)

easyRNASeq 1.6.3

• Added a plotDispLSD function that adds a density estimate color map to the DESeq plotDispEsts function.

easyRNASeq 1.6.2

• Released the constraint on the gtf annotation file parsing to allow for gtf file without the "exon_number" attribute such as those retrieved from UCSC.

easyRNASeq 1.6.1

• Adapted the package dependency
• Added a check to stop processing whenever annotation are outside of the chromosomes.

easyRNASeq 1.6.0

• No changes, Bioconductor release version 2.12

easyRNASeq 1.5.1

• Adapted the dependencies version to match the Bioconductor release version 2.11 BUG FIXES
• corrected an innapropriate function call to an internal function (as in stable version 1.4.2)

easyRNASeq 1.5.0

• No changes, Bioconductor development version 2.12

easyRNASeq 1.4.2

BUG FIXES

• corrected an innapropriate function call to an internal function

easyRNASeq 1.4.1

• Adapted the dependencies version to match the Bioconductor release version 2.11

easyRNASeq 1.4.0

• No changes, Bioconductor release version 2.11

easyRNASeq 1.3.14

NEW FEATURES

• easyRNASeq now returns a SummarizedExperiment in an effort to consolidate the objects used for Next Generation Sequencing in Bioconductor. This is the new default of the count function. The count function is a new function to supersed easyRNASeq in the coming development version (1.5.x) to consolidate the parameters and output of the easyRNASeq function.

BUG FIXES

• corrected a validity check that went permissive.
• changed the print method to display the read length range when dealing with variable read lengths rather than every single value.

easyRNASeq 1.3.13

BUG FIXES

• Same correction as in the stable version 1.2.5, but for those already corrected in version 1.3.3.

easyRNASeq 1.3.12

• Providing the 'outputFormat' argument is not necessary anymore, it defaults to matrix (i.e. count table).
• Relaxed the gtf file checking. If the gene_name is absent, the gene_id is used instead.
• Improved some reporting and remove a bottle-neck occuring when there are many sequences in the reference. BUG FIXES
• Ensure that only the matched ranges are returned when reading gapped alignments.
• The library size is more exactly calculated and is the number of aligned reads.
• Corrected a bug in the validity checking that prevented bam files created by different aligners using the same reference to be processed as the reference sequences were not ordered in the same fashion.

easyRNASeq 1.3.11

BUG FIXES

• Fixed a bug in the gtf file handling reported by Mark Robinson.

easyRNASeq 1.3.10

• Some vignette discrepancies have been corrected. Thanks to Richard Friedman for spotting them.
• Providing the 'filesDirectory' argument is not necessary anymore, if the files to proceed are present in the current directory. Indeed, this parameter now defaults to the current directory as can be found out using 'getwd()'. BUG FIXES
• Fixed a bug introduced by a change in the IRanges coverage function return value.

easyRNASeq 1.3.9

• Added the manuscript citation.
• Updated the package version dependencies. BUG FIXES
• Improved the support for reads of different lengths.
• A cosmetic change to report read lengths as well when read files with variable read length are processed.
• Corrected a bug and enhanced the loading of gtf annotation files. Thanks to Tomasz Kulinski for spotting the issue and providing the dataset to reproduce it.

easyRNASeq 1.3.8

NEW FEATURES

• Now bam files can be processed in parallel (long time request from Wade Davis). If the easyRNASeq argument 'nbCore' is greater than 1 (1 being the default), then that many core will be used to process the read files in parallel. Pay attention not to use too many cores and have enough memory available. The memory load scales up linearly with the number of files processed.

easyRNASeq 1.3.7

NEW FEATURES

• easyRNASeq now supports read of different lenghts. Thanks to Mark Robinson for the toy dataset.
• Added a function that lists existing organism conversion when applying the validity checks.
• Added a bp.coverage to the fetchCoverage function that defaults to FALSE. To allow for variable length reads, it now returns read coverage proportion per bp by default.
• Added additional checks in the .checkArguments internal function.

BUG FIXES

• Not a real bug, but more a consolidation. When an organism is unknown and no custom.map is provided, then the validity checks are turned off and a warning is emitted.
• Providing the chr.sizes as as list has been deprecated. Only named numeric vector are supported.
• Removed a now useless warning in the .readGffGtf function.
• Modified the RPKM function generic to avoid using a 'protected' word as argument: i.e. 'unique' was replaced by 'simplify'

easyRNASeq 1.3.6

NEW FEATURES

• It is now possible to pass arguments to list files through the three dots. I.e. setting recursive=TRUE is now possible.

BUG FIXES

• Corrected a bug in the .getArguments internal function.

easyRNASeq 1.3.5

NEW FEATURES

• bam is now the default format for the easyRNASeq method.
• chromosome sizes are now extracted from the BAM header when the 'chr.sizes' argument is set to "auto". Thanks to Simon Anders for pushing that off my TODO list and the nice implementation.

BUG FIXES

• Adapted to an API change of the edgeR package for estimating the tagwise dispersion.

easyRNASeq 1.3.4

NEW FEATURES

• Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that. Same change as in the stable version 1.2.3
• Ensure that gtf with non Ensembl ID are correctly parsed as well.

easyRNASeq 1.3.3

• Converted the package to use Roxygen2, a Doxygen like in-source documentation system for generating the RD and NAMESPACE. The original man page were converted using the Rd2roxygen package and the resulting in-source documentation manually edited. NEW FEATURES
• Added a type accessor for Genome_intervals object
• Added a coercion to GRangesList from Genome_intervals object BUG FIXES
• Adapted to the new arguments of the edgeR estimateTagwiseDisp function
• Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct.

easyRNASeq 1.3.2

BUG FIXES

• Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this.

easyRNASeq 1.3.1

NEW FEATURES

• Added an enhanced read length check (same as stable 1.2.1 change)

easyRNASeq 1.3.0

• New development version for Bioconductor 2.11

easyRNASeq 1.2.5

BUG FIXES

• Corrected a bug in the condition file name checking.
• When using edgeR, it was not possible to de-activate the drawing of the quality assessment plots.
• Some edgeR changes to the API have been ported to the stable R version, should not have occured... The following are changes that adapt to that new API, changes ported from version the easyRNASeq development version 1.3.3...
• Adapted to the new arguments of the edgeR estimateTagwiseDisp function
• Removed the dispersion.method argument from the plotMeanVar edgeR method call as this argument is defunct.

easyRNASeq 1.2.4

• Added the manuscript citation.
• Updated the package version dependencies.

easyRNASeq 1.2.3

NEW FEATURES

• Added an additional validity check for chromosome names Thanks to Simon Anders for generating a reproducible use-case for that.
• Ensure that gtf with non Ensembl ID are correctly parsed as well.

easyRNASeq 1.2.2

BUG FIXES

• Corrected a bug that was considering a GTF file as a GFF file. Thanks to Simon Anders for spotting this.

easyRNASeq 1.2.1

NEW FEATURES

• Added an enhanced read length check

easyRNASeq 1.2.0

• Stable version released as part of Bioconductor 2.10

easyRNASeq 1.1.10

NEW FEATURES

• Added a naPositionFilter extending ShortRead srFilters

BUG FIXES

• Worked on Wade Davis case with 3 different sets of chromosome names in the three different input (reads, annotation, chromosome sizes)
• Worked on smoother error handling when not using bam files. Again through Wade Davis example
• Ensured that chromosome names conversion occurs whether provided with a factor or a character vector
• extended the NAMESPACE

easyRNASeq 1.1.9

BUG FIXES

• Added an \alias{RNAseq} to ease the class documentation access; an H.Pages suggestion
• Changed the DESCRIPTION file to make sure that the latest ShortRead (1.13.13) and BiocGenerics (0.1.11) package are required

easyRNASeq 1.1.8

BUG FIXES

• Corrected the last occurence of the deprecated matchMatrix call
• Corrected an issue on windows raised by the parallel package. Thanks to Wade Davis for pointing that one out.

easyRNASeq 1.1.7

BUG FIXES

• Fixed the NAMESPACE and the vignette generation

easyRNASeq 1.1.6

BUG FIXES

• Thanks to Francesco Lescai, a bug was fixed. Namely I was not expecting the chromosome names in the bam files and in the chromosome name lists to be two different set with a common intersect. I always consider that one would be the subset of the other one. Now, when such situation occurs only the common set is kept and used for the calculations.
• Herve Pages changed the findOverlaps value. It is now an object of the Hits class that does not support the matchMatrix accessor anymore. The code was adapted to the new accessor queryHits.
• Corrected the package structure to add a vignettes sub-directory. Moved the relevant files there

easyRNASeq 1.1.5

BUG FIXES

• Removed the fitInfo method extension to the DESeq package as it as been implemented in that package
• Reworked the plotDispersionEstimates and .normalizationDispatcher function to deal with the new fitInfo function (the information is stored in an environment rather than in a list)

easyRNASeq 1.1.4

• Package introduced in Bioconductor