Changes in version 1.8.1                        

Miscellaneous

  - Change maintainer's email address.

                        Changes in version 1.7.1                        

Enhancements

  - New plotting function draw_heatmap to produce heatmaps of
    (normalized) counts.

Miscellaneous

  - The utility function df_cols_to_factor now also converts existing
    factors to having explicit missing levels.
  - Version bump on forcats dependency.
  - Removed ggplot2 deprecation warning ..count...

                        Changes in version 1.0.1                        

  - Additional version argument for connect_biomart to specify an
    Ensembl version.
  - Fixed tests.

                        Changes in version 1.0.0                        

  - First BioConductor release.

                       Changes in version 0.99.4                        

  - Corrected authors.

                       Changes in version 0.99.2                        

  - First public release of the hermes package.
  - Submission to BioConductor.

Enhancements

  - Better legends on the genes barplot and the correlation heatmap.
  - Improved vignette layout using the BioConductor style.

Miscellaneous

  - New utility function cut_quantile for cutting a numeric vector into
    quantiles.
  - New utility function cat_with_newline for concatenating and printing
    with newline.
  - New check function check_proportion which checks for a single
    proportion.
  - Better legends on the genes barplot and the correlation heatmap.

                        Changes in version 0.1.1                        

New Features

  - New function draw_scatterplot to produce scatterplots of two genes
    or gene signatures.
  - New function draw_boxplot for boxplots of gene expression values.
  - New function draw_barplot for barplots of dichotomized gene
    expression counts into two or three percentile categories.
  - New helper function wrap_in_mae that wraps a single
    SummarizedExperiment object into an MAE object.
  - New method rename that makes renaming columns of rowData and colData
    as well as assay names in existing SummarizedExperiment objects much
    easier, as a step before converting to HermesData.
  - New method lapply that allows user to apply a function on all
    experiments in a MultiAssayExperiment.
  - New method isEmpty that checks whether a SummarizedExperiment object
    is empty.
  - New gene filtering option n_top in the calc_pca function, which
    allows filtering genes with greatest variability across samples.
  - New class GeneSpec for specification of genes or gene signatures,
    see ?gene_spec for simple construction. Inclusion of gene signature
    functions colPrinComp1 and colMeanZscores to supplement standard
    column statistics functions.
  - New helper function col_data_with_genes which extracts the sample
    variables saved in colData together with selected gene information
    as a combined data set.
  - New helper function inner_join_cdisc which joins genetic with CDISC
    data sets.

Bug Fixes

  - normalize() now also works when the hermes package is not loaded,
    i.e. you can use it with hermes::normalize().
  - correlate() now also works when there are factor variables in the
    sample variables of the HermesData object.
  - add_quality_flags() does no longer return NA as the technical
    failure flags for the samples if there is only a single gene
    contained in the input, but instead a vector of FALSE to ensure
    correct downstream functionality.

Miscellaneous

  - Updated LICENCE and README with new package references.
  - The multi_assay_experiment now contains HermesData experiments,
    different patient IDs, one experiment with normalized assays, and
    multiple samples per patient in one experiment.
  - The main HermesData example is now saved in the package as
    hermes_data, and the previous summarized_experiment is still
    available. Note that patient IDs have been changed in the new
    version to align with the multi_assay_experiment.
  - Renaming of required rowData and colData columns to be more
    consistent with standards and use lowercase snake-case names.
  - Annotation querying and setting is now more flexible in that it also
    allows to query more annotations than the required ones.
  - Instead of gene starts and ends, the total length of gene exons is
    now used as the annotation column size. Corresponding queries from
    BioMart are used to return this gene size.
  - df_char_to_factor has been deprecated (and can still be used with a
    warning) and replaced with df_cols_to_factor, which also converts
    logical variables to factor variables.
  - When providing SummarizedExperiment objects containing DelayedMatrix
    assays to the HermesData() constructor, these are silently converted
    to matrix assays to ensure downstream functionality.

                        Changes in version 0.1.0                        

  - First internal release of the hermes package, which contains
    classes, methods and functions to import, quality-check, filter,
    normalize, and analyze RNAseq counts data for differential
    expression.
  - hermes is a successor of the rnaseqTools R package. The core
    functionality is built on the BioConductor ecosystem, especially the
    SummarizedExperiment class. New users should first begin by reading
    the "Introduction to hermes" vignette to become familiar with the
    hermes concepts.

New Features

  - Import RNAseq count data into the hermes ready format.
  - Annotate gene information from the Ensembl database via biomaRt.
  - Add quality control (QC) flags to genes and samples.
  - Filter and subset the data set.
  - Normalize the counts.
  - Produce descriptive plots.
  - Perform principal components analysis.
  - Produce a templated QC Rmd report.
  - Perform differential expression analysis.