Changelog

Source: NEWS.md

psichomics 1.28.1 (4 Feb, 2024)

• Update GTEx data download based on new URL endpoints
• Documentation:
  • Update function documentation based on bug fixes below
  • Update license copyright years
• Bug fixes:
  • Fix deprecated used of size in ggplot2::geom_line
  • Fix inconsistent argument in survfit.survTerms()
  • Fix unit test issues when testing low coverage using random PSI values
  • Update pkgdown and R CMD check automation in GitHub Actions

psichomics 1.24.0 (26 Oct, 2022)

• Bug fix: psichomics app now opens as expected instead of crashing

psichomics 1.22.1 (14 July, 2022)

• Bug fix: GTEx data v8 can now be downloaded using newer versions of R
• Bug fix: UniProt REST API call now uses the updated API
• Bug fix: Updated deprecated setting to remove ggplot2 guide
• Documentation: Clarify how to get survival plots in CLI tutorial

psichomics 1.20.2 (13 March, 2022)

• Bug fix: fix limma-trend approach when using newer versions of limma to calculate average gene expression

psichomics 1.20.1 (25 January, 2022)

• Bug fix: allow to perform correlation analysis after being performed once

psichomics 1.20.0 (27 October, 2021)

• Alternative splicing event annotations:
  • Support new annotations from VAST-TOOLS for multiple species, including mouse, zebrafish, fruit fly, chicken, frog, C. elegans and A. thaliana
  • Automatically create cache directory if downloading splicing annotations for the first time
• Gene, transcript and protein annotation (visual interface):
  • Automatically set species/genome based on selected annotation
  • Improve species and genome selection

psichomics 1.18.6 (4 October, 2021)

ShinyProxy support

• psichomics(): add argument shinyproxy; when set to TRUE, change set of options to viably run in ShinyProxy
• Avoid automatically closing the app
• Replace custom file browsers with shiny’s versions
• Fix issues with progress bar
• Include ShinyBS JavaScript library
• Upload files using default file browser input and allow to upload a ZIP folder instead of a folder

Bug fixes

• Fix issues with Shiny 1.7.0:
  • Change icon names as required by newest versions of font-awesome
  • Avoid modifying Shiny tags using generic positions
• Load recount data (visual interface):
  • Improve responsiveness of project selection
• Splicing annotation (visual interface):
  • Load annotation only when opening the splicing quantification tab
  • Automatically select hg38 if using GTEx v8 data
• PCA plot (visual interface):
  • Automatically plot PCA after calculating PCA scores
  • Copy-edit text
  • Fix specific errors related with PCA analysis of only one group
• Diagrams of alternative splicing events:
  • Fix wrong coloring of reference exon used for AFE and A5SS events
• Transcript plot:
  • Orange region (the reference exon) is now on top of blue region

psichomics 1.18.5 (24 August, 2021)

• Diagrams of alternative splicing events:
  • Fix wrong coloring of reference exon used for AFE and A5SS events
• Transcript plot:
  • Avoid alternative regions from overlapping
  • Fix loading twice when selecting a new event (visual interface)

psichomics 1.18.4 (22 July, 2021)

• psichomics(): fix visual interface not launching
  • getGtexReleases() not properly retrieving whether future GTEx releases (9 and higher) are available
• Remove warning related with TCGA data when MD5 checks fail

psichomics 1.18.3 (11 June, 2021)

• plotSplicingEvent(): avoid opening browser window in non-interactive contexts
• Fix Bioconductor build report’s timeout when creating vignettes on Windows

psichomics 1.18.1 (26 May, 2021)

• Fix issues with unit tests in Bioconductor
• Improve Docker images:
  • Simplify Dockerfile
  • Store Docker images in GitHub Container Registry
  • Automatically build latest Docker image based on last release version
• Improve README with install instructions for GitHub and Docker
• Minor copy-editing of user-provided data tutorial
• Fix minor spelling issues

psichomics 1.18.0 (18 May, 2021)

• discardLowCoveragePSIvalues(): improve performance (2x faster)
• When quantifying or loading PSI values, psichomics discards splicing events whose junctions:
  • 1. are not present in junction quantification data or
  • 2. have low numbers of reads across all samples. The number of discarded events is now displayed during PSI quantification.
• When normalizing gene expression, support converting gene identifiers to gene symbol names for any species with OrgDb data
• Allow to use plotSplicingEvent() directly with a PSI table to plot diagrams of the alternative splicing events within
• Distribution plots (plotDistribution()):
  • Plot sample distributions in density, violin or box plots (argument type in command-line interface)
  • Hide rug plot when showing 500 or more values (by default) to avoid performance issues
  • Add jitter to rug plot (helps to discern numerous points)
  • Display interquartile range (IQR) per group in the tooltip
  • Add subtitles (argument subtitle in command-line interface)
  • Allow to invert axes (argument invertAxes in command-line interface)

Bug fixes and minor changes

• loadLocalFiles(): print elapsed time after loading local files
• filterGroups() was modified to return a character vector whose names are original names (instead of groups) and include an attribute Groups with the respective group of each value (together with their colour, if available):
  • Distribution plots in the graphical interface now show sample name in the tooltip for each sample
• Importing VAST-TOOLS annotation:
  • Fix parsing of VAST-TOOLS intron retention events as skipped exon for certain annotations (including Hs2)
  • Support diagrams for intron retention events with full exon coordinates
• Graphical user interface improvements:
  • Avoid “Matching subjects to their samples/Matching process concluded” loop
  • Timeout GTEx data retrieval after 3 seconds without server response
  • Avoid unnecessary messages when loading FireBrowse interface
  • Fix intron retention diagrams in distribution plots not displaying introns
  • When searching for specific splicing events, fix results based on the wrong genomic coordinates
• Improve tutorials

psichomics 1.14.4 (30 August, 2020)

• Improve file browser dialog:
  • Now correctly allows to select a single file in macOS
  • Now correctly allows to select a directory in Windows
  • Correctly set default location when opening a file in Linux
  • Internal improvements
• Data loading:
  • Improve performance when loading compressed data (GZ and BZ2 files)
  • Increase optional verbosity while loading files
  • Speed up loading of VAST-TOOLS’ inclusion levels
  • Fix loading of VAST-TOOLS’ inclusion levels sometimes returning an error regarding duplicated row names
  • Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS’ inclusion levels
• Copy-edit tutorials on loading user-provided data and using the command-line version

psichomics 1.14.3 (21 August, 2020)

• Fix unit tests due to changes in Ensembl API response

psichomics 1.14.2 (11 August, 2020)

Support for loading more data formats

• getSplicingEventData(): get a table with all information for a given dataset of alternative splicing quantification data
• VAST-TOOLS inclusion levels and gene expression tables:
  • Import VAST-TOOLS’ output files (inclusion levels, cRPKMs and gene read count tables); in the visual interface, use the User-provided data loading panel and load a specific alternative splicing quantification or load the folder containing such file; in the command-line interface, use loadLocalFiles()
  • To parse splicing event from VAST-TOOLS in the command-line interface, use for instance parseSplicingEvent("HsaEX0007927", data=VASTTOOLSpsi)
• Support for importing inclusion tables with arbitrary alternative splicing event identifiers (information for these events will not be available, such as event type and cognate gene)
• SRA metadata:
  • Automatically load metadata from the SRA Run Selector (usually comes in files named SraRunTable.txt) avoiding the need to use prepareSRAmetadata() first
• GTEx data loading (loadGtexData()):
  • Support for loading GTEx data from V8, V7, V6 or V4 releases
  • Organise GTEx data into folders named based on release version
• Copy-edit tutorial on loading user-provided data

New features

• plotSplicingEvent():
  • Alternative splicing diagrams now render automatically instead of showing SVG code (if printing more than one event, a table is displayed with event identifiers and respective diagrams)
  • Plot intron retention events (e.g. from VAST-TOOLS)
• plotLibrarySize(): plot library size from gene expression data
• Alternative splicing quantification filtering (visual interface):
  • New panel to allow filtering already loaded alternative splicing quantification based on event types, samples, PSI statistics (such as median, variance and range) and cognate genes (some filtering steps may not be available when using user-provided tables with inclusion levels)
  • Filter data based on individual PSI values (also available when quantifying alternative splicing)
  • Filter VAST-TOOLS events based on its quality scores for read coverage
  • Toggle specific statistics based on alternative splicing quantification values when filtering
  • Preview the original and filtered events in an easy-to-use plot
• Gene expression filtering:
  • Toggle specific statistics based on gene expression values when filtering (visual interface)
  • Arguments used in filterGeneExpr() and normaliseGeneExpression() are now returned as attributes of those functions
• Differential analysis:
  • Tooltips of volcano plots now include diagram of alternative splicing events
• Gene, transcript and protein annotation (visual interface):
  • Suggest genes based on loaded data
  • Change species and assembly when fetching information
  • Improve interface of PubMed article query, including persistent user-inputted tags even when changing selected gene
  • Improve relevance of results from PubMed articles
• Much faster calculation of row/column-wise means, medians, variances and ranges (helpful for plotting statistics of large datasets)
• Include Dockerfile to create Docker images based on code revisions

Bug fixes and minor changes

• Progress bar is now animated as in previous versions
• Data loading (visual interface):
  • Allow to discard selected files in file browser input elements
  • When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
  • “Browse…” button now opens file browser to select folder where data is stored (as expected) in GTEx and SRA panels
  • Only pre-create groups of genes (based on literature-based gene lists) if at least one of its genes exists in any of the loaded datasets
  • Correctly parse gene symbols containing underscores
  • Fix gene expression summary plots not showing in specific situations
  • Fix library size plot not working properly and causing rendering issues
  • Fix settings used to quantify alternative splicing not showing up
  • Show errors raised while reading a file (e.g. if file is too big for available memory)
  • Show alert if no GTEx data options are selected
  • Show filename of the file used to load gene expression and alternative splicing data from GTEx and SRA
  • Show helpful context messages in panel interfaces
  • Improve visual interface and minor copy-editing
• Local data loading:
  • Support loading data from GTEx V8 or previous releases
  • Fix bad formatting of help tooltips when using shiny 1.4.0 or newer (visual interface)
• Gene expression filtering:
  • Hide message regarding the usage of no design matrix
• Alternative splicing annotation:
  • Try to load cached alternative splicing annotation if a timeout occurs
  • Include gene symbols in custom annotations if available
  • Account for possible filename changes when parsing annotations from VAST-TOOLS, rMATS, SUPPA and MISO
• Alternative splicing event selection (visual interface):
  • Include loading indicator while searching for events
  • Decrease number of operations performed after selecting an event
  • Fix crash when changing to an alternative splicing quantification dataset without the selected splicing event
  • Allow to search using an event identifier directly
  • Show event identifier instead of prettier identifier to avoid confusion
• Data grouping (visual interface):
  • Simplify group selection interface
  • Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
  • Show an alert when there is no data to create groups
• Dimensionality reduction:
  • performPCA() and performICA() now directly raise errors (instead of simply capturing and returning them)
  • PCA: loading plots now show parsed information of events (cognate gene, event type and genomic position) if available
  • PCA: the correct splicing event is now selected when clicking on any loadings in the loadings plot (visual interface)
• Differential analyses (visual interface):
  • Use group colours in density plots of differential expression table
  • Fix occasional crash when performing differential analyses with different number of groups during the same session
  • Tooltips of volcano plots are now properly positioned in high-resolution screens
  • The correct splicing event is now selected when clicking the density plots or survival curves in the table
  • When creating a group from differential splicing results, correctly set cognate genes of alternative splicing events
  • diffAnalyses(): deprecated psi argument was now removed
• Distribution plots (plotDistribution()):
  • After hiding all plot series, hide Y axis (rug plots of the different groups have arbitrary Y values to easily distinguish them)
  • Rug plots of gene expression density plots are now placed near the X axis as expected
• Correlation analyses (visual interface):
  • Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app)
• print() extended to better display information on gene list objects; e.g. print(getGeneList())
• Fix issues when installing the package:
  • Fix error when unit testing in R 4.0 or higher (strings in data frames are not converted to factors by default)
  • Fix R CMD check warning of Unicode symbol translation in Windows
  • Fix comparing signed and unsigned integers in Rcpp functions

psichomics 1.14.1 (16 June, 2020)

Fix unit tests for R 4.0

psichomics 1.12.1 (29 January, 2020)

• Alternative splicing events can now be represented via diagrams:
  • Redesign of alternative splicing event selection (graphical interface)
  • plotSplicingEvent() plots diagram representation of alternative splicing events
  • In the visual interface, alternative splicing event diagrams were added below distribution plots (to quickly illustrate higher and lower values of alternative splicing quantification) and in annotation page
• User-provided junction quantification loading:
  • Support junction coordinates from mitochondrial, Z and W chromosomes
  • Fix issues with files containing splice junctions within random, alt and unknown chromosomes by discarding those rows (a warning is raised)
• Alternative splicing annotation:
  • listSplicingAnnotations() can now be filtered by species, assembly and data of available annotations
• Improve import/export of data groups from/to a file, including colour support
• Copy-edit and improve all tutorials, welcome message and help tab
• Include link to article in Methods in Molecular Biology: https://doi.org/10.1007/978-1-0716-0301-7_10

More bug fixes and minor changes

• TCGA and SRA data loading:
  • loadFirebrowseData() now returns expected data when asking for multiple datasets (such as in the case of performing a pan-cancer analysis) in both visual and command-line interface
  • SRA projects containing only one column of extra information in sample metadata are now correctly loaded instead of raising an error (loadSRAproject())
• Data loading and manipulation:
  • Copy-edit information on the format of user-provided files
  • Warn when discarding rows with duplicated rownames after loading user-provided files
  • getGtexDataTypes() is now exported, as expected
  • parseSplicingEvent() now returns the coordinates as numeric if coords = TRUE and char = FALSE
  • Improve dialog when trying to load a local folder without any supported files available
• Alternative splicing annotation:
  • Confirmation dialog is not displayed any more when creating a folder (specially useful while running the visual interface)
  • Allow to select cache directory of AnnotationHub (command-line interface)
  • Fix prepareGeneQuant() discarding the argument strandedness if either stranded or stranded (reverse)
• Data grouping:
  • Samples not associated with any subject are now kept when exporting groups to a file
  • Fix issues related with importing groups based on a file with groups of splicing events and/or genes
  • Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
  • Show number of genes contained in pre-made gene lists
  • Discard unavailable genes when creating group of genes based on pre-made gene lists (unless these are automatically created at startup)
• Density plot (plotDistribution()):
  • Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
  • After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
  • Rug plot labels now show data values if sample names are not provided
  • Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
  • Fix misguiding example in function documentation
  • When hovering the values in the rug plot, the colour of the tooltip is now the same used for the rug points as expected
• Survival analysis (p-value plot):
  • Fix alternative splicing quantification cutoff being selected based on the one whose difference has the highest (instead of the lowest) p-value
  • Fix plot line label presenting “p < 0.05” independently of the threshold used for significance
• Gene, transcript and protein annotation:
  • Show available annotation information and query PubMed even if Ensembl is down
  • Avoid app crash when searching for PubMed articles too many times
• Improve warning/error alerts:
  • Fix alerts crashing the visual interface
  • Improve message formatting regarding HTML-containing alerts
• Improve unit tests and function documentation

psichomics 1.10.2 (4 Oct, 2019)

Fix warnings in Windows-specific CI tools and Bioconductor

psichomics 1.10.1 (19 Sep, 2019)

Avoid timeouts in CI tools and Bioconductor builds by skipping a specific unit test

psichomics 1.8.3 (21 April, 2019)

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

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() 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

psichomics 1.8.1 (3 December, 2018)

• Add tag ImmunoOncology to BiocViews

psichomics 1.6.2 (2 October, 2018)

• 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), i.e. 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

Bug fixes and minor changes

• Improve file browser input in remote servers:
  • Allow to directly input a path without using the file browser dialog
  • Display warning when calling the file browser dialog in RStudio Server or in an unsupported system
• TCGA data:
  • Inform of sequencing technology used to obtain gene expression data
• GTEx data:
  • Fix issues in downstream analyses when using GTEx data subset by tissues
• Differential analysis:
  • Avoid limiting X axis of density plot when values outside 0 and 1 are provided, as in the case of gene expression (plotDistribution() function)
  • Fix filenames of exported tables from differential expression analysis incorrectly mentioning differential splicing analysis instead
• Correlation analysis:
  • When plotting correlation analysis, loess curve was performed based on gaussian fitting, independent of the “family” argument of plotCorrelation()
• Improve console logging of error and warning messages

psichomics 1.6.1 (5 July, 2018)

• Improve support for analysing SRA and user-provided data:
  • New tutorial on performing alternative splicing analysis using SRA and user-provided 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

psichomics 1.4.5 (4 Apr, 2018)

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

psichomics 1.4.4 (12 Feb, 2018)

• 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 the 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

psichomics 1.4.3 (12 Jan, 2018)

• 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

psichomics 1.4.2 (19 Dec, 2017)

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

psichomics 1.4.1 (14 Dec, 2017)

• 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

psichomics 1.4.0 (22 Oct, 2017)

• Support for loading new GTEx V7 data
• Support gene expression data:
  • Load, filter, normalise and perform log2-transformation on gene expression data from TCGA
  • Perform principal component analysis based on gene expression data, survival analysis by gene expression cutoff and pairwise differential gene expression analysis
  • Correlate gene expression of a given gene against PSI values of multiple alternative splicing events
• Data loading:
  • Add step-wise instructions about loading of user-provided files
  • Filter GTEx junction quantification based on tissues of interest (all tissues are loaded by default)
  • Quantify splicing based on a list of genes (splicing events within all genes are quantified by default)
  • Parse sample information from TCGA samples using parseTcgaSampleInfo()
  • Generate TCGA sample metadata when loading TCGA junction quantification
  • Present data summary after loading the data
• Data grouping:
  • Redesigned group creation and selection
  • Create groups based on genes and alternative splicing events
  • Assign a customisable colour per data group
  • Export or import patient and sample identifiers of data groups
  • Add new set operations when grouping (such as complement, subtraction and symmetric difference)
  • Suggest attributes of interest when creating groups
  • Allow to retrieve the universe of patient and sample identifiers by performing the complement group without any group selected
  • Statistically analyse group independence (useful to assess the overlap between a PCA cluster and groups derived from clinical and sample attributes, for instance)
• Differential analysis:
  • Label points based on top differentially spliced events or genes, selected alternative splicing events and/or selected genes
  • Create AS event and gene groups based on filtered or selected AS events and genes in the tables
• Dimensionality reduction techniques:
  • Subset data based on groups of AS events and genes before performing dimensionality reduction
  • Create data groups based on the partitioning clustering of PCA scores
  • Perform independent component analysis (ICA) on alternative splicing quantification and gene expression data
• Survival analysis:
  • Add p-value plot to visually infer the significance of survival analyses based on multiple alternative splicing quantification cutoffs
• Gene, transcript and protein information:
  • Information retrieval is now only dependent on a user-defined gene, instead of requiring alternative splicing quantification data to be loaded

Bug fixes and other improvements

• Show progress bar when running in the command-line interface
• Fix inconsistent browser history navigation
• Updated the CLI vignette with information on analysing gene expression data and a quick reference for functions
• Update minimum version required of shiny (1.0.3)
• Avoid replacing selected groups when manipulating new ones
• Differential splicing analysis:
  • Fix data not being rendered in the table when zooming in the plot after data transformation was applied
  • Return p-value of NA instead of 0 when the value of Fligner-Killeen’s Test for Homogeneity of Variance is infinite
  • Discard value transformations that may return invalid data for the values chosen for the X and Y axes
  • Fix point that remains highlighted in the plot after deselecting the only selected row of the table
  • Improve readability of plot’s tooltip
  • Improve survival curves based on the optimal alternative splicing quantification cutoff:
    • Include the survival curve previews in 3 new columns within the differential splicing analyses table, instead of below that table; those columns consist of the survival curves, the optimal PSI cutoff and the respective log-rank test’s p-value
    • Allow to use survival data when plotting and table sorting
    • Include the optimal PSI cutoff and the respective log-rank test’s p-value in exported tables
    • Fix link to survival analyses using the previously calculated PSI cutoff
• Principal component analysis:
  • When clicking on a alternative splicing event in the loadings plot, the appropriate differential splicing analyses will now be automatically rendered with the respective options, as expected
• Survival analysis:
  • Properly set the title of survival curves based on the selected splicing event’s quantification
  • Improve readability of Cox PH models
  • When performing survival analyses by alternative splicing cutoff, each patient is assigned the PSI value from the respective sample; for patients with more than one sample, the assigned sample is chosen based on the most frequent sample type across all patients (before, the first matched non-normal or non-control samples were used)
• Multiple other bug fixes and visual improvements

psichomics 1.2.1 (24 Apr, 2017)

• Gene, protein and transcript information:
  • Fix missing file required for transcript plots
• Update command-line interface tutorial to render a transcript plot

psichomics 1.2.0 (22 Apr, 2017)

• Gene, protein and transcript information:
  • Fix tooltip text presentation in transcript plot
  • Fix JavaScript issues when zooming the transcript plot
  • Fix error when plotting events associated with multiple genes
  • Fix error when plotting single-exon transcripts
  • Protein name, length and function are now presented when available
  • Improved general presentation of the information
• Differential splicing analyses:
  • Click and drag in the plot to zoom in and subsequently filter events shown in the table
  • Decreased step of sliders
  • Improve interface of previewed survival curves
  • When clicking on a table link to navigate to differential splicing analyses of a single event, the appropriate analyses will now be automatically rendered with the respective options, as expected
• Settings (renamed to “Help”):
  • Add links to tutorials and user feedback
  • Add app information and acknowledgements
  • Remove unused option for choosing cores (all performed operations are still single-core, given the difficulty of working with multi-processes in Shiny)
• Improve dialogues regarding missing data and other minor interface elements
• Update documentation with volcano plot

psichomics 1.0.9 (10 Apr, 2017)

• Differential splicing analyses:
  • Add volcano plot to represent events through selected attributes, such as p-values and descriptive statistics (e.g. median and variance) between groups of interest
  • Transform values of the X and Y axis in the plot using log transformed, inverted and absolute values, for instance
  • Highlight events in the plot based on values of the X and Y axis
  • Table of differential analyses per alternative splicing event is filtered according to highlighted and selected events in the plot
• Gene, protein and transcript information:
  • Transcript plot is now interactive and zoomable
  • Protein are now rendered based on selected transcript alone
  • Faster parsing of UniProt’s web API response
  • Improve display of article information when data is missing
• Principal component analysis:
  • Improve presentation of available options
• When clicking on previews of differential splicing and survival analyses, the appropriate analyses will now be automatically rendered with the respective options
• Fix buggy browser history when the user is directed to a different tab
• Consistently use FireBrowse and Firehose across the package
• Update documentation

psichomics 1.0.8 (21 Feb, 2017)

• Support GTEx data loading and analysis
• Fix clinical data dependency:
  • Fix error when trying to load a file containing alternative splicing quantification without first loading clinical data
  • Fix error where samples from junction quantification were matched to clinical information even if clinical data were not loaded
  • Inform user when clinical data is not loaded while trying to plot survival curves
• Improve data grouping:
  • Create sample groups like patient groups and perform set operations between any created groups
  • Create groups using patient and sample identifiers
  • Check number of patients and samples per group
  • Rename selected groups
  • Alert user when groups cannot be created due to missing data
• Differential splicing analysis:
  • Analyse all samples as one group
• Survival analysis:
  • Select any clinical attribute for starting/follow up and ending times
• Create table containing TCGA sample metadata when calculating or loading alternative splicing quantification
• Minor UI improvements

psichomics 1.0.7 (22 Jan, 2017)

• Survival analysis:
  • Fix error caused by some non-matched patients not being in the patient-sample matching matrix

psichomics 1.0.6 (17 Jan, 2017)

• Update tutorials with more relevant and complex examples
• Update minimum versions required of highcharter (0.5.0) and shiny (1.0.0):
  • Fix function usage as according to new version of highcharter
  • More options available when exporting plots (PNG, JPEG, SVG, XLS and CSV)
• Faster alternative splicing quantification
• Differential splicing analysis:
  • Fix major bug where samples could be placed in the wrong groups
  • Shorten speed of the calculation for the optimal PSI cutoff that minimises the survival difference
  • Fix not performing statistical tests for two selected sample types while analysing a single event with three or more sample types
  • Fix differential analysis on one splicing event not working when using diffAnalyses()
  • Fix differential analysis not showing for individual events before navigating to the page where the analysis is performed for all events
  • Improve readability and information of statistical tests for single events
• Principal component analysis:
  • Shorten time taken to calculate principal components and to render the loadings plot
  • Fix loadings plot error when rendering some principal components
• Survival analysis:
  • Fix incorrect number of patients from the survival groups in the contextual information for the selected cutoff (below the slider)
  • Improve how alternative splicing quantification is assigned to patients based on their samples
• Protein annotation:
  • Warn user when trying to render proteins with no domains

psichomics 1.0.5 (7 Jan, 2017)

• Navigate history using the browser forward and back buttons
• Fix delay when displaying large data by removing columns containing missing values exclusively
• Principal component analysis:
  • Improve speed when calculating total contribution of each variable to the principal components
• Survival analysis:
  • Shorten calculation of optimal PSI that minimises the survival difference
  • Improve visual cues of optimal PSI cutoff and present p-value of selected PSI cutoff
  • Fix ambiguous error messages
  • Fix incorrect Cox model results for formula-based calculations
  • Fix null Cox models crashing the program
• Differential splicing analysis:
  • Select sample types for differential splicing analysis
  • Fix statistical tests not displaying for individual events after differentially analysing all events using the other statistical tests

psichomics 1.0.4 (18 Dec, 2016)

• Correctly load files and quantify alternative splicing for PRAD, OV and PAAD tumour types from The Cancer Genome Atlas (TCGA)
• Fix session disconnecting when exporting plots in Firefox
• Improve text and behaviour of fields to select datasets and AS events
• Fix author names and add contributor

psichomics 1.0.3 (13 Dec, 2016)

• Bug fixes regarding gene annotation:
  • Fix disabled gene selection when choosing a splicing event associated with a single gene after selecting an event related to multiple genes
  • Fix display of PubMed articles related to previously selected gene when selecting a single-gene-associated event after selecting an event related to multiple genes
• Bug fixes regarding groups:
  • Fix groups by rows not working
  • Fix group selection not working when only one group exists
  • Improve argument name of getGroupsFrom()
• Other minor improvements

psichomics 1.0.2 (3 Dec, 2016)

• Fix UTF-8 encoding in author list

psichomics 1.0.1 (1 Dec, 2016)

• Improve metadata (title, description, authors and vignette titles)

psichomics 1.0.0 (5 Oct, 2016)

• First release of psichomics
• Quantify, analyse and visualise alternative splicing data