Version 1.8
psichomics 1.8.2 (26 March, 2019)
- Data loading:
- GTEx data can now be automatically downloaded and loaded on-demand
- By default, data table now only displays at most the first 100 columns for performance reasons
- Alternative splicing quantification:
- Allow to discard samples before alternative splicing quantification
- In alternative splicing quantification dataset summary, plot quantification based on median, variance and range per splicing event across samples to provide tools to filter quantification (
plotRowStats()
)
- Gene expression filtering and normalisation:
- Allow to discard samples before filtering and normalisation
- Filter low read counts using
edgeR::filterByExpr()
- Allow to perform
limma::voom()
on gene expression data (without design matrix) and to apply its normalisation methods - In gene expression dataset summary, plot distribution of gene expression per sample, distribution of library sizes and gene-wise mean and variance of gene expression across samples to provide the user tools to assess gene expression normalisation (
plotGeneExprPerSample()
,plotDistribution()
andplotRowStats()
, respectively) - Convert between different gene identifiers (the original identifier is kept in some conditions, read
convertGeneIdentifiers()
); in the visual interface, when filtering and normalising gene expression, ENSEMBL identifiers are converted to gene symbols, by default
- Groups:
- By default, load pre-made lists of genes when loading gene expression or loading/performing alternative splicing quantification
- Added pre-made list of genes that encode for RNA-binding proteins (Sebestyen et al. 2016), useful to postulate about the regulatory role of those proteins based on gene expression and PSI correlation analyses
- Correlation analyses:
- Allow to use groups of genes and alternative splicing events in correlation analyses
- Plot specific combinations of gene and alternative splicing events (
[.GEandAScorrelation
()) - Display progress when performing correlation analyses
- Display correlation results in a table (
as.table()
)
- Survival:
- Render p-value plot by cutoff in command-line interface (
plotSurvivalPvaluesByCutoff()
)
- Render p-value plot by cutoff in command-line interface (
- Gene, transcript and protein information:
- Modify keywords used to search for PubMed articles
Bug fixes and minor changes
- Improve console logging of error and warning alerts
- Fix crash when loading psichomics with test data that is not locally available (by automatically downloading said data if not found)
- Allow to edit file path in file/directory browser elements
- Documentation:
- Export functions mentioned in the documentation
- Hide documentation of internal functions from the PDF reference manual
- Loading SRA data:
- Accept a vector of files as the first argument (easier to use with
list.files()
) - Ask to overwrite file if one exists with the same name as the output file
- Accept a vector of files as the first argument (easier to use with
- Groups:
- Automatically set dropdown width for group attribute selection
- Minor improvements to the group creation interface
- Fix error when creating groups containing only samples and no matching subjects
- Fix warning when displaying group preview only based on subjects or samples
- Alternative splicing quantification:
- Automatically set the human genome version after loading data from TCGA (hg19), GTEx (hg19) or recount2 (hg38)
- Fix progress bar
- Decrease loading time after quantifying alternative splicing
- By default, quantify skipped exons, mutually exclusive exons, alternative 3’ and 5’ splice sites, and alternative first and last exons; the default option is now consistent across both the visual and command-line interfaces)
- Differential analyses:
- Allow distribution plots to show the name of the samples when hovering or when a rug plot is rendered if
rugLabels = TRUE
(functionplotDistribution()
) - Fix distribution plots requiring all samples in a group when using function
plotDistribution()
- Fix group colours and opacity for rug plot points within the distribution plot (occurred in the command-line version; function
plotDistribution()
) - Fix wrong information in the table of differential splicing results (only occurs when the first splicing event is one for which there is not enough information to calculate statistical tests)
- Fix inconsistency when presenting median and variance differences between gene expression and alternative splicing quantification
- Fix error when groups contain samples outside the data being analysed
- Allow distribution plots to show the name of the samples when hovering or when a rug plot is rendered if
- Gene, transcript and protein information:
- Fix article title formatting (e.g. bold and italics)
- Update psichomics citation with journal publication date
psichomics 1.8.3 (21 April, 2019)
Replace deprecated R.utils::evalWithTimeout()
with R.utils::withTimeout()