NEWS.md
In hbc/bcbioRnaseq: Bcbio RNA-Seq

Release notes

Minor changes:

Fix for extract ([) method, where drop argument must appear at the end.
Migrated bcbioRNASeq generator unit test that imports GFF file to longtests, as this can be slow to download from Ensembl FTP server.

Minor changes:

Updated functional analysis template for potential breaking change with EnsemblToNcbi step, which no longer supports format argument.

Major changes:

We're now enforcing strict camel case for function names.

Minor changes:

Resaved example bcb object.
Renamed plotGeneSaturation to plotFeatureSaturation in QC template.
Renamed plotGenesDetected to plotFeaturesDetected in QC template.
Renamed plotMeanSD to plotMeanSd in QC template.
Renamed plotPCA to plotPca in QC template.
Renamed plotRRNAMappingRate to plotRrnaMappingRate in QC template.
Renamed plotMA to plotMa in DE template.
Renamed plotDEGPCA to plotDegPca in DE template.
Renamed plotDEGHeatmap to plotDegHeatmap in DE template.
Renamed Ensembl2Ncbi to EnsemblToNcbi in FA template.

Minor changes:

Now requiring R 4.3 / Bioconductor 3.17.
Reworked internal tximport handling to use new isTximport assert check from the goalie package.

Major changes:

bcbioRNASeq object will now fail validity checks with validObject if entrezId is defined in rowData instead of now preferred ncbiGeneId. This breaking change can be resolved using updateObject.
Fixed breaking change in functional analysis R Markdown template, due to new usage of ncbiGeneId instead of legacy entrezId metadata in GRanges returned by AcidGenomes package.

Minor changes:

Resaved example bcb object using Bioconductor 3.17 dependencies.
Now classing on DFrame and GRanges instead of DataFrame and GenomicRanges virtual classes internally.

Minor changes:

Added transcript identifier sanitization support during tximport call for kallisto aligned against GENCODE reference. Refer to related Bioconductor issue for details.

Minor changes:

Updated dependencies to Bioconductor 3.16.
Migrated requireNamespaces import from AcidBase to goalie.

Major changes:

Reworked functional analysis template.
Reworked R Markdown templates to use level 2 headers by default instead of level 1, to pass markdownlint-cli checks (from Node; can use koopa to install). Our configuration needs to be updated in AcidMarkdown to reflect this change.
Updated unit tests to testthat 3 engine.

Minor changes:

Reworked and resaved example objects.
Reworked quality control and differential expression R Markdown templates slightly, adding lintr exceptions.
Switched to using Map instead of mapply, where applicable.
Now enabling pathview by default in functional analysis template.
Removed sessioninfo as a dependency, switching back to using utils sessionInfo internally instead.
Included some additional reexports to make the package work with F1000v2 manuscript as best as possible.

Major changes:

Starting a new release series requiring R 4.2 / Bioconductor 3.15.
Minor bug fixes to provide compatibilty with Acid Genomics dependencies.

Minor changes:

Now using DataFrame return from metrics by default. Hardened calls to ggplot using as.data.frame coercion.

Major changes:

Now requiring R 4.2 / Bioconductor 3.15.

Minor changes:

Minor S4 class fixes to provide compatiblity with Bioconductor 3.15.
Relaxed version pins in DESCRIPTION file.

Starting a new release series for 2022.

Major changes:

Package now requires R 4.1+ / Bioconductor 3.14+.
Package no longer attaches basejump automatically.

Minor changes:

Removed internal dependencies on formalsList parameters defined in basejump, which will be removed in a pending release update.

Minor changes:

Reworked the default expected file path of bcbioRNASeq object (e.g. "bcb.rds"), which has been moved back to data instead of nested inside of rds by date (e.g. YYYY-MM-DD).
Other R Markdown templates, specifically the differential expression and functional analysis templates have also been updated to reflect this change.
Minimum dependencies have been bumped back to R 4.0 / Bioconductor 3.13 due to current bioconda build issues, which will be resolved in a future update of the package.

Minor changes:

Updated dependencies to require Bioconductor 3.14.
Bug fix for assert check failure of tximport list return. The infReps slot in list does not return named rows when txOut is TRUE for Bioconductor 3.14 release.

Minor changes:

Updated dependencies, in particular now requiring fixed version of DESeqAnalysis that labels genes in plotVolcano call as expected.
Updated comments in functional analysis template.
Added additional suggested packages that are required for R Markdown templates to render when called from a conda environment.

Minor changes:

Improved R Markdown template support, particularly handling of Entrez identifier mapping in the functional analysis template. Also updated pathview code to timeout on very large pathways, such as general metabolism, which can contain hundreds of genes.
Updated unit tests against F1000 example dataset.
Removed usage of magrittr pipe in examples, in favor of base R pipe (4.1+).
Improved internal package name and version handling.
Harden internal tximport handling code a bit.
Main bcbioRNASeq importer now supports a very minimal dataset with a single sample, which isn't common.

Maintenance release, incorporating useful changes from the basejump v0.14 release series.

Minor changes:

Reworked S4 generic imports, migrating some functions to AcidGenerics.
Reduced the number of dependency packages, since we can offload some of the imports to basejump.
Switched from cli to AcidCLI (via basejump) internally.
Note that internal GenomicRanges utilities (e.g. makeGRangesFromEnsembl) need to have ignoreVersion = TRUE defined, since this argument changed by default in AcidGenomes.

Minor changes:

Bug fix for featureCounts directory structure change in bcbio v1.2.4 release.
Wrapped DESeq2 normalization calculations (to be defined in assays slot) in a tryCatch call, to more gracefully avoid errors on minimal data sets, such as the bcbio-nextgen unit test data.

Minor changes:

Maintenance release, updating minimum dependency package versions.

Minor changes:

Hardened plotting functions against bcbioRNASeq objects created with fast = TRUE.
show: Added display of fast: TRUE when applicable.
Documentation updates.

Minor changes:

Decreased R package dependency versions a bit, so we can update the bioconda recipe successfully. Some Bioconductor packages don't have point release updates on bioconda.

Minor changes:

Maintenance release, updating minimum R dependency to 4.0.

Minor changes:

Temporarily disabled plotPCACovariates, which causing CI checks to error due to a dplyr bug in DEGreport. Will reenable when this gets fixed and is updated on Bioconductor.

Minor changes:

bcbioRNASeq generator now has improved message support for selected samples. Internally, this is managed by the cli package.
updateObject: Now supporting verbose argument, which defaults to FALSE.

Minor changes:

bcbioRNASeq: Removed now defunct spikeNames argument. Refer to makeSummarizedExperiment documentation and release notes in basejump package for details.

Minor changes:

Relaxed validity checks against dataVersions and programsVersions in metadata slot, for compatibility with updateObject upgrade path from v0.2.9 objects, which are currently generated by bcbio-nextgen. Thanks @sjmonkley for catching this. See issue #146.
Changed license from MIT to GPL-3.
Updated documentation.

Major changes:

Improved internal handling of bcbioRNASeq to DGEList coercion, for handoff to edgeR and limma-voom. Now the code handles countsFromAbundance settings more intelligently and informs the user whether downstream edgeR and/or limma-voom handoff is appropriate.
Now exporting as.DESeqDataSet, as.DESeqTransform, and as.DGEList S4 generic methods, which support arguments. Note that quick coercion using only as (see coerce documentation from Bioconductor) does not support arguments.

Minor changes:

Fixed support for bcbio fastrnaseq pipeline. Thanks to @kokyriakidis for pointing this out. Added code coverage support for an example run produced via this pipeline.
Updated basejump dependencies, namely renaming bioverbs to AcidGenerics.
Now using cli package for improved messages.

Minor changes:

Added support for Bioconductor 3.10.
Updated internal DataFrame validity checks to also check for DFrame class, which has changed in latest S4Vectors 0.23 release.
Updated basejump dependency versions.

Minor changes:

Reworked quality control plots to use "labels" instead of "title".
Updated R Markdown templates and added render code coverage in testthat-extra.
Updated vignette to use shared bibliography.bib file from basejump.

Minor changes:

bcbioRNASeq: Internal generator now calls importSampleData using pipeline = "bcbio" argument, so we don't run into breaking changes when handling user metadata in a future basejump update.
Updated basejump dependency versions.

Minor changes:

Now requiring R 3.6, as we near a candidate Bioconductor release.
Updated basejump dependencies.

Major changes:

Made subsetting factor for extract ([) operations.
updateObject: Improved rowRanges handling.

Minor changes:

bcbioRNASeq generator now captures call using standardizeCall instead of match.call, and automatically expands all default arguments.
Improved NAMESPACE and basejump dependencies.
Made vsn and DEGreport packages optional, to reduce the number of dependencies required for installation.
plotPCACovariates: Reworked internal code to not depend on dplyr.
Removed internal code dependencies on magrittr pipe.

Minor changes:

Simplified internal object creation in bcbioRNASeq, [, and updateObject.
Improved message consistency.

Major changes:

updateObject: Worked internal approach to be compatible with upcoming Bioconductor 3.10 release. Has to rethink the strategy to handling assays internally, which can no longer be easily coerced from assays slot in the bcbioRNASeq object, due to changes in ShallowSimpleListAssays handling. This should return an object in exactly the same manner as previous releases.

Major changes:

bcbioRNASeq: Now supporting fast argument, which enables the user to skip any internal DESeq2 calculations. This will skip generation of normalized, vst, and fpkm matrices. Note that automatic rlog matrix generation is no longer supported, since it's often too slow, especially for large datasets. If you want to generate rlog counts, simply coerce the bcbioRNASeq object to a DESeqDataSet, then run the rlog function.
Aligned counts are now saved inside the object when a pseudoaligner (e.g. salmon, kallisto) are used to define the primary counts assay. These values are saved in an aligned matrix.

New functions:

pseudoVsAligned: Visually inspect the correlation of pseudoaligned counts to the aligned counts. Note that default bcbio genomes use legacy UCSC builds, where as the pseudoaligners generate values from newer Ensembl transcript annotations.

Minor changes:

Updated package dependency versions.

Major changes:

Initial support for bcbioRNASeq to DGEList (edgeR) object coercion.
relativeLogExpression: Improved internal code, using edgeR calcNormFactors approach.

Minor changes:

Updated basejump dependency to v0.10.11.
Improved Travis CI docker config to check coverage and lints.
Improved Bioconductor installation instructions.

Minor changes:

Added support for size factor adjusted counts as "sf" in counts call.
Improved internal trans axis labeling handling for DESeqTransform counts.
plotMeanSD: Improved default colors. Improved internal non-zero count handling. Reworked plot headers.

Major changes:

Now pinned to R >= 3.5.

Minor changes:

Improved Travis CI and AppVeyor CI configuration.

Minor changes:

S4 generic reexport documentation fixes.

Minor changes:

Bar plots now show the first sample at the top of the Y axis when flip = TRUE. This is more human readable.
Quality control template now uses bcbiornaseq_file as main input param.
Bug fix: added back internal .normalizedTrans function required for some quality control plots.

Minor changes:

Tweaks to quality control template.
Switched Travis CI configuration to use rnaseq Docker image.

Minor changes:

Ensuring that all basejump functions necessary for the quality control template get reexported.
Renamed R Markdown template files and travis-render.sh script into kebab case, rather than snake case.
Documentation improvements (using inheritParams).

Moved forked development repository to Acid Genomics.

Major changes:

Switched unit testing data URL from seq.cloud to acidgenomics.com.

Minor changes:

Reworked internal reexports for assignment generics. See counts for example.
Miscellaneous documentation improvements.
Switched from basejump prefix to acid, where applicable.
Reexported essential functions from basejump required for QC template to render without basejump being attached.

Minor changes:

Added additional checks to bcbioRNASeq validity method.
Draft update to quality control template, to support parameterized bcbioRNASeq object input. This is likely not necessary and will be removed in a future update.
Added additional checks for bcbioRNASeq to DESeqDataSet coercion.
Improved internal perMillion argument code handling inside plotting functions: plotMappedReads, plotTotalReads.
Removed reexports.R. No longer reexporting Gene2Symbol or magrittr pipe.

Major changes:

sampleData: Moved method support to basejump package.

Minor changes:

Resaved example data.
Sample metadata chunk in quality control template now returns DataFrame.
Improved some deprecation messages.
CI configuration improvements.

Minor changes:

Renamed plotGene to plotCounts, to match consistency in basejump and DESeqAnalysis package updates.
Updated dependencies to provide improved backwards compatibility support for R 3.4 / Bioconductor 3.6.

Minor changes:

Travis CI build configuration and documentation fixes.

Minor changes:

Bug fixes for interestingGroups handling in plotting functions. Needed to add back an interestingGroups<- assignment call to slot the object.
Removed sanitizeRowData and sanitizeSampleData from imports.

Minor changes:

.tximport: Use makeNames to check for valid names internally.
Improved documentation.
Travis CI configuration fixes to get build checks to pass.

Major changes:

Overhauled validity method for bcbioRNASeq. Improved check steps using ok method, similar to approach in goalie.
Added back plotPCACovariates method support.

Minor changes:

Updated pkgdown configuration. Removed alphaSummary, contrastName, export, markdown, sampleData, topTables
goalie package has been updated to support nullOK mode where applicable. This is particularly use for formals that use NULL by default. See bcbioRNASeq generator changes, for example.
prepareRNASeqTemplate example is causing build checks to fail, so disable.
Improved CI configuration.

This is the first release that switched over to using goalie for assert checks instead of assertive.

Major changes:

bcbioRNASeq generator has been overhauled to use assert for assert checks.

Minor changes:

Ensure title is quoted in R Markdown.
Switched to using validate in place of validate_that in validity checks.
Miscellaneous documentation improvements.
Now using match.arg internally to check validity of countsFromAbundance argument passthrough to tximport.

Major changes:

Added additional improvements to quality control template. Ensuring that setup chunk never caches. bcbioRNASeq object should be called using params$object_file. This convention will be used across all other bcbio R packages. Reworked and simplified plotCountsPerGene section of QC template.

Minor changes:

Added early return method for objects without modification extract method. Might want to reconsider this approach if the user just wants to reorder samples. We're checking for unmodified return by looking for identical raw counts matrix before and after extraction call.
plotCountsPerBiotype: Ensure normalized argument uses "tpm" first.
plotDispEsts: Switch to using hasUniqueCols internally instead of areSamplesUnique.

Major changes:

Improved and simplified quality control template. Removed Dropbox mode (which may be added back in a future update). Identical samples detection is now supported automatically in the plotting functions, which was previously defined in the QC template.
Improved subset sample handling inside extraction method. Extraction method now imports useful relevelRowRanges and relevelColData utilities from basejump.

Minor changes:

Removed sampleData<- reexport.
Documentation fixes and improvements, particularly to the bcbioRNASeq generator function.
Reworked internal gffFile handling inside bcbioRNASeq generator function.
Simplified passthrough in internal .new.bcbioRNASeq call.
plot5Prime3PrimeBias now uses color argument instead of fill.
plotDispEsts now checks for duplicate samples and early returns.
Consistently use British spelling variants (colour instead of color) for ggplot2 functions. Our formals will stick with American English though.
plotTotalReads: Bumped recommended default to 20 million from 10 million.

Minor changes:

Added additional library loads to _setup.R: rmarkdown, basejump, DESeq2.
plotGene: Updated working example.
Improved reexport of sampleData<- generic.
Updated Travis CI configuration.

Major changes:

Splitting out new DESeqAnalysis S4 class to a separate package.

Deprecated functions and methods:

Functions removed from NAMESPACE: magrittr pipe (%>%), DESeqAnalysis, DESeqResultsTables, alphaSummary, contrastName, export, markdown, plotDEGHeatmap, plotDEGPCA, plotMA, plotMeanAverage, plotVolcano, topTables.
alphaSummary: Migrated DESeqDataSet method to DESeqAnalysis package.

Example data:

Deleted deseq example, which has migrated to DESeqAnalysis package.

Minor changes:

Reorganized internal assert checks.
Miscellaneous documentation improvements.
Improved consistency of global formals (using getOption) via formalsList global variable.

Major changes:

Improved validity method for bcbioRNASeq S4 class.
extract ([) method: Improved internal handling of rowRanges and colData. Now using I internally for complex S4 columns in mcols for rowRanges.
Reworked imports back to basejump instead of attempting to use subpackages: basejump.annotations, basejump.assertions, basejump.classes, basejump.coerion, basejump.developer, basejump.experiment, basejump.generics, basejump.globals, basejump.io, basejump.markdown, basejump.plots, basejump.sanitization. Rethink this approach in a future update.

Minor changes:

Resaved example bcb dataset.
Miscellaneous internal assert check fixes and updates.
Miscellaneous documentation improvements.
Added internal Rle global variable. May want to avoid this approach because Rle is a defined function in S4Vectors, however.
Offloaded some global documentation params to basejump.
Reworked some global params set by getOption in formals.

Development fork of hbc/bcbioRNASeq. Code development will proceed here on the fork until a stable release is ready to merge back at official HBC repo, to avoid any disruption for active RNA-seq experiments.

New S4 classes:

Added new DESeqAnalysis S4 class, which helps containerize up a DESeq2 analysis, often requiring corresponding DESeqDataSet, DESeqTransform, and DESeqResults objects. Note that this class may be defined in a separate package in a future update.

Code migration to basejump:

aggregateReplicates has moved to basejump, and now works primarily on SummarizedExperiment method, instead of bcbioRNASeq.
Offloaded a number of S4 generics to basejump infrastructure, which are now defined in the bioverbs package: alphaSummary, contrastName, plot5Prime3PrimeBias, plotCountDensity, plotCountsPerGene, plotDEGHeatmap, plotDEGPCA, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate.
metrics method, which returns a tbl_df of colData, has been moved to basejump.
plotCorrelationHeatmap code is now primarily defined in basejump as a SummarizedExperiment method. bcbioRNASeq now calls this method internally but keeps support for normalized counts argument.
Removed tpm method support, which is now handled by SummarizedExperiment method support in basejump.

S4 method reworks:

Reworked internal code, splitting out S4 methods into internal functions (e.g. counts.bcbioRNASeq). This step is recommended by Bioconductor, and can make troubleshooting easier.
export: Reworked S4 methods for DESeqResults and DESeqResultsTables S4 classes.
extract (i.e. [) method: Switched transform formal to recalculate. Added additional assert checks. Operation no longer changes the saved version of bcbioRNASeq, slotted into metadata.
interestingGroups formal is now set NULL instead of missing for plotting functions.
markdown: Initial support of new S4 generic, which returns a markdown table of sample metadata.
plot5Prime3PrimeBias: Added an addition grep matching step to handle differential variations on the x5x3Bias column in colData.
plotCountDensity S4 method has been removed. Use plotGeneSaturation generic with geom = "density" argument instead.
plotCountsPerBiotype: New S4 method support, which calls basejump SummarizedExperiment method.
plotDEGHeatmap: Draft update of DESeqResults method.
plotDEGPCA: Draft update of DESeqResults method.
plotDispEsts: Split out and reworked internal method definition.
plotGenesDetected: This code has been moved to basejump and is now defined against SummarizedExperiment.
plotMA: Reworked internal DESeqResults method code. Added draft support for new DESeqAnalysis S4 class. Keeping plotMeanAverage reexported, since this function is used in the F1000 workflow paper.
plotMappingRate: Set the default limit back down to 0.7.
plotMeanSD: Reworked internal DESeqDataSet code. Added additional assert checks and changed the default handling of vst and rlog internal formals.
plotPCA: Draft update of SummarizedExperiment. Will offload this code to basejump in a future update. Switched return argument to support tibble and S4 DataFrame -- note change from previous support for data.frame.
Deleted plotPCACovariates method, since DEGreport is failing. Will add back support for this generic in a future update.
plotQC: Initial method support for bcbioRNASeq.
plotTotalReads: Reworked and tightened up internal ggplot2 code.
plotVolcano: Draft update to DESeqResults method. Will rework this code with a DESeqAnalysis approach in a future update.
relativeLogExpression: Added S4 method support.
resultsTables: Removed this approach to subsetting DESeqResults. This will be a rework in the upcoming DESeqAnalysis package.
sampleData: Simplified internal code, which takes advantage of updates to SummarizedExperiment defined in basejump.
updateObject: Reworked internal metadata handling.

Example data reorganization:

Renamed and simplified example datasets. Now only exporting bcb (bcbioRNASeq) and deseq (DESeqDataSet) examples.
bcb_small, dds_small, gender_markers, and res_small have been removed.
Updated and consolidated corresponding data-raw/ scripts.
Reworked internal extdata/bcbio/ example datasets. Testing out both 2017-05-23_rnaseq and 2018-03-18_GSE67267-merged data.

R Markdown templates:

Stripped down supported R Markdown templates. Currently simplified code base to support Quality Control markdown (quality_control). Differential expression and functional analysis templates have been temporarily removed but will be re-added in the future.

Minor changes:

Reorganized S4 class definitions and validity checks in AllClasses.R. Previously, this code was split out per S4 (e.g. bcbioRNASeq-validity.R).
Moved S4 coercion methods from coerce-methods.R to as-methods.R.
Added internal assert checks in assert-internal.R.
Consolidated internal DESeq2 code into DESeq2-internal.R.
Consolidated and defined additional global variables into globals.R.
Reorganized internal .meltCounts code.
Consolidated global package parameter arguments into params.R.
bcbio prefix has been renamed to basejump, where applicable. Refer to global function params defined with getOption, and internal ggplot2 utility functions, such as basejump_geom_abline.
Draft support for countsFromAbundance selection in internal tximport call. This is useful for some transcript-level analyses.

Deprecations:

Removed defunct download function.
New deprecations: plotCountDensity, plotPCACovariates, resultsTables.

Minor changes:

Update to support basejump v0.10+ release series.

Major changes:

Fixed a bug in internal tximport code (refer to tximport-internal.R file) where sample names can get associated with the wrong samples in experiments, causing samples with numbers roll over from 1 -> 10. Thanks to Richard from AstraZeneca for catching this.

Handle correlation of PCA covariates when a numerical covariate has no variation.
Handle NA in ribosomal RNA calculations.

Minor changes:

Bug fix for as coercion method support. Need to ensure exportMethods(coerce) is included in NAMESPACE file, otherwise bcbioRNASeq to DESeqDataSet coercion using as(bcb, "DESeqDataSet") won't work when called from an Rscript without the package library loaded. Thanks @roryk for noticing this.
Only run rRNA plots if rRNA is detected.

Major changes:

Added transform = TRUE argument to [ extraction method, allowing the user to skip automatic DESeq2 transformations, which can be CPU intensive for large datasets.
Switched back to using plotMA instead of plotMeanAverage. An MA-plot by definition is not a "Mean Average" plot, so this function name is misleading. We will keep the plotMeanAverage working but it is now soft deprecated.
plotGeneSaturation now supports label argument, similar to plotPCA.

Minor changes:

Improved internal handling during tximport call to handle transcript version mismatch with tx2gene data.frame. This can result if the bcbio pipeline is using an old genome build.
Ensure genomeBuild is detected from AnnotationHub rowRangesMetadata if applicable, and not left NULL in the metadata.
Updated internal code to use aes instead of aes_string, which uses tidyeval and quasiquotation.
plotGene: reduced the number of return options to simply "facet" and "wide". Previously, this also supported "grid", "list", and "markdown", but these were removed because they are not frequently used.
plotGene: Switched back to internal lapply call instead of using BiocParallel::bplapply. This doesn't always work perfect in an HPC environment (e.g. HMS O2 cluster).
Soft deprecated plotMeanAverage in favor of plotMA.
All S4 generics with method support are exported for easier lookup in the reference documentation.
All function reexports have been consolidated in bcbioBase package.

Minor changes:

Enable support bcbio integration, by modifying bcbioRNASeq constructor to work with minimal bcbio test data.
Switched from internal usage of aes_ in favor of consistent usage of aes_string. This will make the transition to ggplot2 v2.3.0 easier in a future update.

Major changes:

aggregateReplicates support has been added back. This function returns a RangedSummarizedExperiment instead of a bcbioRNASeq object, containing only an aggregate raw counts matrix in the counts slot of assays.
The functional analysis R Markdown template has been reworked to use dds_file and organism as new parameter arguments. We've reduced the number of parameters required here to run clusterProfiler.
Made alphaSummary defunct for bcbioRNASeq object, in favor of DESeqDataSet only. This function is only useful when a proper design formula has been defined.

Minor changes:

metrics now contains an informative error for datasets that were analyzed using the fast-rnaseq bcbio pipeline.
DESeqDataSet coercion from bcbioRNASeq object doesn't attempt to run DESeq command any more, which was unnecessary and improves speed.
bcbioSingleCell constructor now supports censorSamples parameter. This is useful for removing known poor quality samples upon loading.
ggplot2 color and fill palettes are now set NULL in the quality control functions. This behavior doesn't change the appearance of the plot colors, which will still default to ggplot2::scale_colour_hue or ggplot2::scale_fill_hue. The upcoming ggplot2 v2.3.0 update supports global options for color and fill palettes, so these parameters may be deprecated in a future release.
Reworked the internal code for topTables.

Infrastructure changes:

Added macOS testing to Travis CI build checks.
Fixed clusterProfiler compilation error on Travis CI by installing libudunits2-dev (Linux).

Major changes:

Now recommending variance stabilizing transformation (vst) over rlog counts by default in plots, where applicable.

Minor changes:

Tweaked Rory's biotype plots in QC report to match formatting conventions in the package. These plots are now colored.
Added plotDEGPCA to default differential expression R Markdown template.
colData factors are correctly releveled upon object subset with [. This helps avoid unwanted downstream errors when creating a DESeqDataSet and running differential expression with DESeq2.
Recommending facet return method by default for plotGene. Updated the working example to reflect this.
metrics now returns interestingGroups column.
sample label has been removed from axis title for QC plot functions.
Now using shared ggplot2 convneience functions from bcbioBase 0.2.10: bcbio_geom_abline, bcbio_geom_label, and bcbio_geom_label_repel. These are also used by bcbioSingleCell for improved graphical consistency.
Removed unused internal legacy ggplot2 code.
Increased DEGreport, DESeq2, and tximport dependency requirements.

Minor changes:

Split out assertive imports so we can pin on bioconda.
Improved package documentation.
Improved label consistency in plotPCA functions to match plotMeanAverage and plotVolcano.
Improved automatic title labeling in plotDEGPCA, matching the other DEG functions. Also added directionality to plotDEGPCA.
Added DESeqDataSet method support to plotCorrelationHeatmap, using the normalized counts.
reusltsTables now writes local files to tempdir when Dropbox mode is enabled using dropboxDir.

Last set of code fixes before F1000v2 resubmission.

Major changes:

Added rle return support for counts, which are calculated on the fly.
Added transgeneNames and spikeNames support to loadRNASeq function.
loadRNASeq now supports organism = NULL again, for datasets with poorly annotated genomes.
Primary assay containing raw counts is now named counts instead of raw, for consistency with other SummarizedExperiment objects (e.g. DESeqDataSet) and the bcbioSingleCell S4 class definition.
Improved internal code for plotGene and plotGenderMarkers.

Minor changes:

Improved AppVeyor CI support to test against bioc-devel using R 3.5.
Improved support and unit testing for updateObject method.
DESeq2 normalized counts are always slotted in assays, even when rlog and vst transformations are skipped.
Exporting [[<-, assays<-, colData<-, interestingGroups<-, and metadata<- assignment methods, to avoid unwanted coercion to SummarizedExperiment. Objects extending RangedSummarizedExperiment shouldn't be doing this, so we may need to file a bug report with Bioconductor or check our class definition in the package.
Now importing specific functions from S4Vectors and methods rather than importing everything.
Switched back to using stop, warning and message rather than the alternate [rlang][] functions abort, warn, and inform.
Objects with invalid metadata now print which slots are invalid to the console.

Major changes:

bcbioRNASeq S4 class object is now extending RangedSummarizedExperiment instead of SummarizedExperiment. Consequently, the row annotations are now stored in the rowRanges slot as GRanges class, instead of in the rowData slot as a DataFrame. The rowData accessor still works and returns a data frame of gene/transcript annotations, but these are now coerced from the internally stored GRanges. The GRanges object is acquired automatically from Ensembl using basejump::ensembl. By default, GRanges are acquired from Ensembl using AnnotationHub and ensembldb. Legacy GRCh37 genome build is supported using the EnsDb.Hsapiens.v75 package.
assays now only slot matrices. We've moved the tximport data from the now defunct bcbio slot to assays. This includes the lengths matrix from tximport. Additionally, we are optionally slotting DESeq2 variance-stabilized counts ("rlog", "vst"). DESeq2 normalized counts and edgeR TMM counts are calculated on the fly and no longer stored inside the bcbioRNASeq object.
colData now defaults to returning as data.frame instead of DataFrame, for easy piping to tidyverse functions.
bcbio slot is now defunct.
FASTA spike-ins (e.g. EGFP, ERCCs) can be defined using the isSpike argument during the loadRNASeq data import step.
Melted counts are now scaled to log2 in the relevant quality control functions rather than using log10. This applies to plotCountsPerGene and plotCountDensity. Note that we are subsetting the nonzero genes as defined by the raw counts here.
Simplified internal tximport code to no longer attempt to strip transcript versions. This is required for working with C. elegans transcripts.
Minimal working example dataset is now derived from GSE65267, which is also used in the F1000 paper.
Added as(object, "DESeqDataSet") coercion method support for bcbioRNASeq class. This helps us set up the differential expression analysis easily.
counts function now returns DESeq2 normalized counts (normalized = TRUE) and edgeR TMM counts (normalized = "tmm") on the fly, as suggested by the F1000 reviewers.
Design formula can no longer be slotted into bcbioRNASeq object, since we're not stashing a DESeqDataSet any more.
Updated Functional Analysis R Markdown template.

Minor changes:

validObject is now required for all plotting functions. This check is also called in the R Markdown template. Legacy objects can be updated using updateObject.
metrics now returns columns sorted alphabetically.
Added contrastName as a generic function.
plotDEGHeatmap and plotDEGPCA generics no longer have counts defined in the signature. The counts argument is now only defined in the methods.
prepareRNASeqTemplate has been converted from a generic to a standard function.
Improved metadata validity checks.
plotCorrelationHeatmap matrix method has been moved to basejump package, for improved consistency with the other heatmap code.
plotGenderMarkers internal code has been reworked to match plotGene.
Default plotMA appearance has changed, providing a line at the 0 y-intercept, similar to DESeqDataSet method.
Internal example datasets have been renamed (e.g. bcb_small instead of bcb).
Added AppVeyor CI support for code testing on Windows.
Made Travis CI checks stricter, added BiocCheck.
Internal .sampleDirs code is now exported in bcbioBase as a generic.
gene2symbol and interestingGroups method support are now defined for SummarizedExperiment in the bcbioBase package.

Updating legacy objects (pre v0.2.0):

Use updateObject in combination with the rowRanges argument, which requires a GRanges object. GRanges can be obtained from Ensembl using the basejump::ensembl function or the ensembldb package.

Deprecations:

bcbio slot is now defunct, since we have moved all data into the SummarizedExperiment container.
Deprecated plot5x3Bias in favor of plot5Prime3PrimeBias. This is less confusing as to what this function plots.
flatFiles has been deprecated in favor of as(object, "list") coercion method. See bcbioBase package for SummarizedExperiment method support.
Defunct: design, download, meltLog10, txi.
Legacy bcbioRNADataSet method support has been removed.

Bug fix for gene2symbol argument not renaming rows in plotDEGHeatmap.

Bug fix for [ subset method dropping metrics in metadata.
Simplified unit testing for Dropbox mode enabled in resultsTables.

Bug fix for gene-to-symbol mappings in plotDEGHeatmap.
Added support for quickly plotting differentially expressed genes (DEG) in a PCA plot with plotDEGPCA.
Added support for Dropbox shared links to resultsTables, for use with the Stem Cell Commons database.
Added assert checks internally for all functions.
Improved internal code for plotGene and plotGenderMarkers to run faster.
Deprecated data frame methods based on metrics for QC functions.

Import shared dependency functions from bcbioBase instead of basejump.
Added method support for selectSamples.
organism and genomeBuild parameters are now user-definable in the main loadRNASeq import function.
Fixed gene subsetting method on S4 object, which handles genes using intersect in the featureCounts matrix.
Removed internal aggregateReplicates code. This needs to be reworked and added back in a future release.
Improve method for handling a missing normalized counts matrix in the assays slot. This can occur when the user opts to skip the CPU-intensive DESeq2 normalizations.
Improved internal code for the quality control functions. Improved the if statements to be more class specific.
Renamed plotCorrelationHeatmap transform argument to normalized, for consistency with the counts generic.
Added title support to plots, where applicable.
Updated internal code for plotDEGHeatmap.
Updated internal marker handling code for plotGenderMarkers.
resulsTables function now defaults to summary = TRUE.

Migrated all basejump function imports to bcbioBase package.

Combined examples (bcb, dds, res, etc.) into a single examples object. This helps avoid accidental use of example bcb in an analysis.
Moved ggplot imports from internal-ggplot.R to above each function.
Renamed maxSamples parameter in loadRNASeq to transformationLimit. If there are more samples than this limit, then the DESeq2 transformations will be skipped. In this case, rlog and vst will not be slotted into assays.
Added a colData sanitization step in loadRNASeq to ensure rows are in the same order as the columns in the counts matrix. Otherwise, DESeq will report an error at the DESeqDataSetFromTximport step. We're also ensuring the factor levels get updated here.
Now using glimpse instead of str in examples, where applicable.
Added colData<- assignment method support. This requires a DataFrame class object. Upon assignment, the internal colData at bcbio(object, "DESeqDataSet"), assays(object)[["rlog"]] and assays(object)[["vst"]] are also updated to match.
Initial assignment support for design, which will update the internal DESeqDataSet.
Added method support for gene2symbol generic, which will now return a 2 column data.frame with ensgene and symbol columns. This is helpful for downstream gene to symbol mapping operations.
Added working example for interestingGroups<- in the documentation.
Added some code to improve factor releveling, where applicable. See internal-meltLog10.R for example.
Now explicitly defining the custom color palettes (e.g. viridis::scale_fill_viridis(discrete = TRUE). This makes it clearer to the user in the documentation where these palettes are located.
Improved axis label support in plotGene.
plotHeatmap now uses internal gene2symbol mappings from stashed annotable, instead of always querying Ensembl. The user can define custom mappings with the gene2symbol argument, if desired.
plotPCA now supports custom color palettes. The shapes parameter has been removed because it doesn't work well and is limited to datasets with few samples. This behavior matches the PCA functionality in DESeq2.
Improved internal code for plotVolcano. Added support for gene2symbol argument, like in plotHeatmap. If left missing, the function will query Ensembl for the gene2symbol mappings. We're now using data instead of stats as the main data source.
Improved legibility of subset method code.
Added some additional reexports, which are used for the package documentation and website.
Simplified legacy object coercion method code.
Updated Bioconductor installation method code. We're now using the dependencies argument, which allows for automatic install of suggested packages along with imports.

Updated package imports to match Bioconductor 3.6.
Added support for interesting groups assignment with interestingGroups<-.
Renamed plotGeneHeatmap to simply plotHeatmap.
Added gender marker support for Homo sapiens.
Improved support for multiple interesting groups in quality control plots. Now interestingGroups is defined as a column in the metrics data.frame that is used to specify the plot color/fill. This matches the convention in the bcbioSingleCell 0.0.22 update.
Sample metadata columns are now consistently set as factors.

Added support for coloring of multiple interesting groups in quality control plots.

Updated version and author information to match the F1000 Research workflow.
Added an f1000v1 branch containing the reproducible code used to generate the figures in our workflow.
Modified plotMA to support vertical or horizontal layout return. Also added an argument to remove the color legend, which is typically not that informative.
Added custom color palette support to the quality control functions.
Upgrading from bcbioRNADataSet (< 0.1.0) to bcbioRNASeq class object is now possible using as coercion method.
Object oriented methods are now restricted to use bcbioRNASeq object. Legacy bcbioRNADataSet objects must be upgraded to bcbioRNASeq class.

Added support for output of unstructured data inside bcbioRNASeq S4 object using flatFiles function.
Added bcbioRNASeq method support for annotable generic.

Renamed bcbioRNADataSet S4 class to bcbioRNASeq. This matches the naming conventions in the bcbioSingleCell package.
Renamed loadRNASeqRun to simply loadRNASeq.
Switched loadRNASeq from using S4 dispatch to a standard function.
Added a parameter argument to loadRNASeq that enables request of a specific Ensembl release version for gene annotations.
Renamed interestingGroup argument in quality control functions to interestingGroups for better consistency.
Improved handling of sample metrics in plotPCACovariates.
Added functional analysis R Markdown template.
Offloaded some core functionality shared between bcbioRNASeq and bcbioSingleCell to the basejump package. This included some code to handle sample metadata YAML and file loading. This helps provide a consistent experience across both packages.

Renamed package from bcbioRnaseq to bcbioRNASeq.
Improved website appearance.
Added viridis color palette support to quality control functions.
Improved subset operations on bcbioRNADataSet object.
Fixed setup chunk loading of bcbioRNADataSet in differential expression R Markdown template.

Added S4 methods support for plots, allowing the user to use either bcbioRNADataSet or a metrics data.frame and manual interesting_group declaration for visualization.
Migrated function and variable names from snake_case to camelCase.
Offloaded small RNA functionality to a separate package named bcbioSmallRNA.

Reworked R Markdown templates to improve YAML defaults and add more comments.
Modified default path variables in setup.R to use *_dir instead of *_out.
Updated NEWS file to use Markdown syntax.

Slotted DESeqDataSet using design = formula(~1) for quality control. This enables automatic generation of rlog and vst transformed counts.
Documentation fixes and website updates.
Renamed S4 class from bcbioRnaDataSet to bcbioRNADataSet (case sensitive).
Adjusted the number of exported functions.

Added testthat checking with lintr.
Initial setup of code coverage using covr.

Prepared draft of F1000 workflow document.

Added Travis CI support for automatic rendering of quality control report.

bcbioRnaDataSet S4 definition updates.
Updates to plot_pca and gene-level heatmaps.

Simplified count pooling functions.

Reduced number of exports and improved documentation.

Draft migration of bcbio run object into S4 bcbioRnaDataSet.
Created a new variant of load_run that saves to S4 object instead of list.

Reworked and re-organized internal functions.

Defaulted to loading run using project summary YAML file.
Initial commit of R Markdown templates (e.g. quality control).
Added support for dynamic file downloads from HBC website.
Draft build of website using pkgdown::build_site.

Improved RDAVIDWebService utility functions to work with dplyr 0.6.0.

Reworked metadata and summary metrics functions to obtain information from project-summary.yaml saved in the final run directory.

Reduced number of depdencies.
Initial commit of modified volcano plot from CHBUtils package.
Internal code updates for upcoming dplyr 0.6.0/[tidyeval][] update.
Updated Ensembl biomaRt annotations to use live site, currently release 88.

Renamed import_* functions to read_*.

Consolidated NAMESPACE imports.
Defaulted to writing count matrices with gzip compression, to save disk space.

Renamed internal parameters for better readability.
Improved documentation and consolidate functions by group.

NAMESPACE simplification using basejump package.

Reworked handling of plots and tables during knits.

Initial commit of differential expression and gene set enrichment functions.

Added bcbio object integrity checks.
Improved detection and handling of lane split samples.

Reworked functions to utilize bcbio list object.

Added plotting functions.

Start of package development.
Initial draft release supporting automatic loading of bcbio run data.

hbc/bcbioRnaseq documentation built on April 1, 2024, 11:31 a.m.

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hbc/bcbioRnaseq Bcbio RNA-Seq

NEWS.md In hbc/bcbioRnaseq: Bcbio RNA-Seq

Release notes

bcbioRNASeq 0.6.2 (2024-03-27)

bcbioRNASeq 0.6.1 (2023-12-05)

bcbioRNASeq 0.6.0 (2023-10-05)

bcbioRNASeq 0.5.5 (2023-08-19)

bcbioRNASeq 0.5.4 (2023-05-02)

bcbioRNASeq 0.5.3 (2023-02-15)

bcbioRNASeq 0.5.2 (2023-02-08)

bcbioRNASeq 0.5.1 (2022-10-24)

bcbioRNASeq 0.5.0 (2022-05-09)

bcbioRNASeq 0.4.1 (2022-04-29)

bcbioRNASeq 0.4.0 (2022-03-11)

bcbioRNASeq 0.3.44 (2021-12-14)

bcbioRNASeq 0.3.43 (2021-12-13)

bcbioRNASeq 0.3.42 (2021-07-27)

bcbioRNASeq 0.3.41 (2021-07-21)

bcbioRNASeq 0.3.40 (2021-02-23)

bcbioRNASeq 0.3.39 (2020-12-03)

bcbioRNASeq 0.3.38 (2020-10-08)

bcbioRNASeq 0.3.37 (2020-09-15)

bcbioRNASeq 0.3.36 (2020-09-11)

bcbioRNASeq 0.3.35 (2020-07-24)

bcbioRNASeq 0.3.34 (2020-07-08)

bcbioRNASeq 0.3.33 (2020-05-11)

bcbioRNASeq 0.3.32 (2020-02-24)

bcbioRNASeq 0.3.31 (2020-02-19)

bcbioRNASeq 0.3.30 (2020-01-20)

bcbioRNASeq 0.3.29 (2019-10-30)

bcbioRNASeq 0.3.28 (2019-09-17)

bcbioRNASeq 0.3.27 (2019-09-09)

bcbioRNASeq 0.3.26 (2019-08-27)

bcbioRNASeq 0.3.25 (2019-08-20)

bcbioRNASeq 0.3.24 (2019-08-12)

bcbioRNASeq 0.3.23 (2019-07-29)

bcbioRNASeq 0.3.22 (2019-07-23)

bcbioRNASeq 0.3.21 (2019-07-17)

bcbioRNASeq 0.3.20 (2019-05-29)

bcbioRNASeq 0.3.19 (2019-05-05)

bcbioRNASeq 0.3.18 (2019-04-25)

bcbioRNASeq 0.3.17 (2019-04-22)

bcbioRNASeq 0.3.16 (2019-04-17)

bcbioRNASeq 0.3.15 (2019-04-11)

bcbioRNASeq 0.3.14 (2019-04-01)

bcbioRNASeq 0.3.13 (2019-03-29)

bcbioRNASeq 0.3.12 (2019-03-18)

bcbioRNASeq 0.3.11 (2019-02-12)

bcbioRNASeq 0.3.10 (2019-02-01)

bcbioRNASeq 0.3.9 (2019-01-23)

bcbioRNASeq 0.3.8 (2019-01-17)

bcbioRNASeq 0.3.7 (2019-01-13)

bcbioRNASeq 0.3.6 (2018-12-12)

bcbioRNASeq 0.3.5 (2018-12-01)

bcbioRNASeq 0.3.4 (2018-11-29)

bcbioRNASeq 0.3.3 (2018-11-25)

bcbioRNASeq 0.3.2 (2018-11-19)

bcbioRNASeq 0.3.1 (2018-11-14)

bcbioRNASeq 0.3.0 (2018-11-06)

bcbioRNASeq 0.2.10 (2019-05-29)

bcbioRNASeq 0.2.9 (2019-05-03)

bcbioRNASeq 0.2.8 (2019-01-28)

bcbioRNASeq 0.2.7 (2018-08-22)

bcbioRNASeq 0.2.6 (2018-08-19)

bcbioRNASeq 0.2.5 (2018-06-21)

bcbioRNASeq 0.2.4 (2018-05-24)

bcbioRNASeq 0.2.3 (2018-05-10)

bcbioRNASeq 0.2.2 (2018-04-26)

bcbioRNASeq 0.2.1 (2018-04-24)

bcbioRNASeq 0.2.0 (2018-03-22)

bcbioRNASeq 0.1.8 (2018-04-03)

bcbioRNASeq 0.1.7 (2018-02-28)

bcbioRNASeq 0.1.6 (2018-02-20)

bcbioRNASeq 0.1.5 (2018-01-31)

bcbioRNASeq 0.1.4 (2018-11-27)

bcbioRNASeq 0.1.3 (2017-12-03)

bcbioRNASeq 0.1.2 (2017-11-08)

bcbioRNASeq 0.1.1 (2017-10-26)

bcbioRNASeq 0.1.0 (2017-10-23)

bcbioRNASeq 0.0.28 (2017-10-17)

hbc/bcbioRnaseq
Bcbio RNA-Seq

NEWS.md
In hbc/bcbioRnaseq: Bcbio RNA-Seq