1.8.3

Bug fix: Replace deprecated R.utils::evalWithTimeout() with R.utils::withTimeout()

1.8.2

• 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() and plotRowStats(), 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())
• 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
• 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 (function plotDistribution())
  • 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
• Gene, transcript and protein information:
  • Fix article title formatting (e.g. bold and italics)
• Update psichomics citation with journal publication date

1.8.1

Add tag ImmunoOncology to BiocViews

1.6.2

• Update citations to link to article in Nucleic Acids Research: https://doi.org/10.1093/nar/gky888
• Copy-edit README, tutorials, DESCRIPTION, NEWS and code
• Update screen shot
• Add metadata regarding loaded datasets (for instance, path and name of files used for dataset loading, options set upon dataset creation, etc.)
• Differential splicing and expression analysis:
  • Allow to input formulas when highlighting points; this is an improvement when plotting -log10(q-values), for instance, where it is now possible to highlight values >= -log10(0.05), e.g. q-values <= 0.5, instead of inputting an approximate value
• Correlation analyses:
  • Colour samples by group
  • Render contour based on a density estimate
  • Display exportable table with correlation analyses
• Groups:
  • Show group colour in group selection element
• Retrieve articles from PubMed instead of PMC

1.6.1

• Improve support for analysing SRA and user-owned data:
  • New tutorial on performing alternative splicing analysis using SRA and user-owned data from FASTQ files (other tutorials were also updated)
  • Process gene and splice junction counts from STAR output for subsequent loading into psichomics
  • Automatically download and load data from select SRA projects using the recount R package
• Data grouping:
  • Preview groups based on selected attribute before creation
• Gene, transcript and protein information:
  • Display alternative splicing events in transcript plot
• Correlation between gene expression and alternative splicing:
  • Allow to change plot height and font size

Bug fixes and minor changes

• Support new version of Human (hg38 assembly) alternative splicing annotation (fixes wrong coordinates for many minus-strand splicing events)
• Fix issues with TCGA sample metadata:
  • No sample metadata loaded when loading TCGA files from local folder
  • Not retrieving sample metadata for all TCGA samples when multiple junction quantification files are loaded
• Data grouping:
  • Correctly suggest how to select variables in subset expression and give more examples on how to use this feature
  • Fix subject/sample attributes not being updated for selection for the GREP interface
  • Fix error alerts not appearing when trying to create groups based on invalid parameters
  • Add an error alert when trying to extract group data from an user-provided file without such information
• Alternative splicing quantification:
  • Fix crash when quantifying splicing for a single sample
• Differential splicing analysis (exploratory):
  • Fix crash when inputting non-numeric values or minimum larger than the maximum limit as the axes for the splicing scatter plot

1.4.5

• Mention the original article throughout psichomics
• Copy-edit graphical user interface and respective tutorial
• Fix warnings and errors in Bioconductor

1.4.4

• Update CITATION file to show citation to article in bioRxiv: https://www.biorxiv.org/content/early/2018/02/07/261180
• Update vignettes to include a case study based on the aforementioned article
• Gene expression pipeline:
  • Perform limma-trend by default
• Alternative splicing quantification:
  • Quantification of alternative first and last exons: following more thorough testing, the new exon-centred method was considered to be less relevant to exploratory analysis (specially when compared with other types of events); as such, both methods are now available for quantification
• Dimensionality reduction:
  • Change tolerated missing values per event to 5% by default for both PCA and ICA (in both visual and command-line interfaces)
  • PCA: In the table that shows the events that most contribute to the selected principal components, show their respective rank
• Groups:
  • Automatically set sample type groups (i.e. normal, primary solid tumour, metastatic, etc.) for TCGA samples (visual interface only)
• Differential analysis:
  • Use numeric fields instead of sliders to precisely filter data
  • Fix table for differential expression not being filtered based on highlighted genes
  • Filter splicing events or genes to use when performing exploratory differential analyses
• Survival analysis:
  • Allow to stratify patients based on optimal gene expression cutoff
  • Select samples to be used for survival analysis

Bug fixes

• Fix problems related with DT versions >= 0.3:
  • Groups displayed as having the same attributes as last created group
  • Table not being updated in differential analyses according to event filtering based on the volcano plot

1.4.3

• Alternative splicing quantification:
  • Improve speed and memory usage when dealing with larger datasets
  • Improve quantification of alternative first and last exons: quantify alternative first and last exons based on all exon-exon junction reads that support each of the alternative exons
  • Print progress bar in R console
• Principal component analysis:
  • Change tolerated missing values per event to 5% by default
  • Show/save table with the contribution of events (for alternative splicing quantification) or genes (for gene expression) to the selected principal components
  • Add extra information when hovering variables in loading plot
  • Allow to plot top 100 variables that most contribute to the selected principal components (faster rendering of and interaction with loading plots)
• Differential analysis:
  • Allow to input a list of groups for the "group" argument of the functions "diffAnalyses" and "plotDistribution" (command-line interface)
  • Allow to input a non-numeric vector or a row of a matrix/data frame in the "data" argument of the function "plotDistribution" (command-line interface)
• Correlation between gene expression and alternative splicing:
  • Perform correlation between gene expression of multiple genes and quantification of multiple alternative splicing events

Bug fixes

• Fix unnamed events when only one event for a event type is returned
• Minor copy-editing and overall improvements

1.4.2

Fix error when trying to load alternative splicing annotation (given updated hg19 and hg38 annotation in Bioconductor that is now available for use with psichomics)

1.4.1

• GTEx data loading:
  • Add input elements to allow GTEx gene expression loading in the graphical interface
  • Fix bug that did not allow to select tissues to load GTEx v7 data (graphical interface)
  • Fix splicing events not being quantified based on GTEx v7 junction reads
• Gene expression normalisation:
  • Fix misleading gene expression (non-)normalisation by converting reads to counts per million (CPM) using edgeR::cpm after normalisation using edgeR::calcNormFactor
• Alternative splicing quantification:
  • Updated support to properly parse new notation of alternative splicing annotation from Bioconductor (backwards compatible with older notation)
  • Raise error when no splicing events after quantification
  • Fix warning following the quantification of splicing events or its loading (incorrect parsing of gene information from splicing events)
• Dimensionality reduction:
  • Use the number (instead of the percentage) of tolerated missing values per sample as the argument to impute data from the remaining samples for those values before performing dimensionality reduction; by default, missing values are tolerated for 10 samples
• Update file description and README
• Minor bug fixes and improvements