Stable release V3.7.0

3.7.0 (2023-04-07)

This version introduces small RNA read alignment using ShortStack, new filtering functions, a new optional parameter for Principal Component Analysis, improvements to the graphical interface, and bug fixes.

Added

• Added small RNA read alignment using ShortStack (fastq.shortstack_align_smallrna).
• Added new filtering function 'Filter specific rows by name' (Filter.filter_by_row_name).
• Added new filtering function 'Filter rows with duplicate names/IDs' (Filter.filter_duplicate_ids).
• Function parameters in pop-up windows in the graphical interface can now be imported and exported.
• Added new parameter to Principal Component Analysis (CountFilter.pca) 'proportional_axes', that allows you to make the PCA projection axes proportional to the percentage of variance each PC explains.
• Improved clarity of error messages in the graphical interface.

Changed

• Tables loaded into RNAlysis that use integer-indices will now be converted to use string-indices.
• Refactored CountFilter.from_folder into CountFilter.from_folder_htseqcount, and added a new CountFilter.from_folder method that accepts a folder of count files in any format.
• In the RNAlysis graphical interface, optional parameters that can be disabled will now display the hint "disable this parammeter?" instead of "disable input?".
• Added optional parameter 'ylim' to 'create enrichment bar-plot' function (enrichment.enrichment_bar_plot), allowing users to determine the Y-axis limits of the bar plot.
• Updated function signatures of 'Visualize gene ontology' and 'Visualize KEGG pathway' (enrichment.gene_ontology_graph and enrichment.kegg_pathway_graph) to make more sense.
• Removed parameter 'report_read_assignment_path' from featureCounts feature counting (fastq.featurecounts_single_end and fastq.featurecounts_paired_end).
• The RNAlysis graphical interface should now load more quickly.
• Progress bars in the graphical interface should now reflect elapsed/remaining time for tasks more accurately.

Fixed

• Fixed bug in the function 'Split into Higly and Lowly expressed genes' (Filter.split_by_reads) where the two resulting tables would be named incorrectly (highly-expressed genes would be labeled 'belowXreads' and vice-versa).
• Fixed bug where the 'column' parameter of some functions ('Filter by percentile', 'Split by percentile', 'Filter with a number filter', 'Filter with a text filter') would not automatically detect column names in the graphical interface.
• Fixed bug where the 'numerator' and 'denominator' parameters of of the function 'Calculate fold change' would not automatically detect column names in the graphical interface.
• Fixed bug where tables with integer-indices could not be visualized properly through the graphical interface.
• Fixed bug in the function 'featureCounts single-end' (fastq.featurecounts_single_end) where setting parameter 'report_read_assignment' to any value other than None would raise an error.
• Functions that take column name/names as input (transform, filter_missing_values, filter_percentile, split_percentile) can now be applied to fold change tables (FoldCangeFilter objects).
• Fixed bug where the description for the 'n_bars' parameter of the 'create enrichment bar-plot' function (enrichment.enrichment_bar_plot) would not display properly.
• 'Visualize gene ontology' and 'Visualize KEGG pathway' (enrichment.gene_ontology_graph and enrichment.kegg_pathway_graph) now have proper parameter descriptions.
• Fixed bug where in-place intersection and difference in the filtering module would fail when using recent versions of pandas.
• Fixed bug where graphs generated through the Visualize Gene Sets window would not immediately display when using the RNAlysis stand-alone app.

Stable release V3.6.2

3.6.2 (2023-03-25)

This version introduces quality-of-life changes to the graphical interface, as well as bug fixes.

Added

• Sample groupings in functions such as PCA, Pair-plot, etc., can now be imported and exported through the graphical interface.

Fixed

• Fixed bug where the stand-alone Mac version of RNAlysis would sometimes fail to map gene IDs (directly or in enrichment analysis).

Stable release V3.6.1

3.6.1 (2023-03-22)

This version introduces minor bug fixes.

Changed

• DESeq2 automatic installation should now work more reliably.

Fixed

• Fixed bug where PCA plots would not display on the stand-alone app unless another visualization function was applied afterwards.
• Fixed bug where Pipelines that contain specific functions (such as translating gene IDs/filtering biotypes from GTF file) would fail to run through the graphical interface.
• GO Annotations annotated by ComplexPortal are now supported by RNAlysis.

Stable release V3.6.0

3.6.0 (2023-03-07)

This version introduces improvements to the usability and clarity of the graphic interface, new methods for automatic estimation of the number of clusters in a dataset, and various bug fixes.

Added

• Added three new methods for automatic estimation of the number of clusters in a dataset: Callinski-Harabasz, Davies-Bouldin, and Bayesian Information Criterieon.
• Added a 'Close all Figures' actions to the 'View' menu of the RNAlysis graphic interface.
• Added an 'interactive' parameter to Volcano Plots (DESeqFilter.volcano_plot) and 'Scatter Sample Vs Sample' (CountFilter.scatter_sample_vs_sample), allowing user to label data points interactively by clicking on them.
• Added more optional plotting parameters to Volcano Plots (DESeqFilter.volcano_plot) and 'Scatter Sample Vs Sample' (CountFilter.scatter_sample_vs_sample).

Changed

• Progress bars are now integrated into the main RNAlysis window instead of opening as a dialog box.
• Information about running proccesses and functions is now displayed in the main RNAlysis window.
• It is now possible to cancel queued jobs through the RNAlysis graphic interface.
• When loading multiple data tables at the same time, it is now possible to change the table type of all data tables at once, instead of one-by-one.

Fixed

• RNAlysis KEGG enrichment should now match the new KEGG annotation format from March 1st 2023.
• Fixed bug where importing RNAlysis would raise ImportError when cutadapt is not installed.
• Fixed bug where the 'Run' button in the Enrichment Analysis window would grey out whenever the enrichment dataset is changed.
• Fixed bug where the RNAlysis stand-alone versions were unable to export Figures in specific formats (e.g. PDF, SVG).
• Fixed bug where functions that depend on R scripts (such as DESeq2 and limma) would sometimes fail to run on MacOS (thanks to Matthias Wilm and sandyl27 in #12).
• Fixed bug where running limma-voom with a design matrix whose column names contained spaces or special characterse would raise an error.
• Fixed bug where the 'highlight' parameter of CountFilter.scatter_sample_vs_sample would not work when used through the graphic interface.
• Fixed bug where enrichment analysis would sometimes fail to run when 'exclude_unannotated_genes' is set to False.
• Fixed bug where translate_gene_ids() would fail for RankedSet objects.
• Fixed bug where filtering gene sets by user-defined attributes (FeatureSet.filter_by_attribute()) would occasionally fail to run.

New Contributors

• [sandyl27] in [#12]

Stable release V3.5.2

3.5.2 (2023-02-23)

This version includes bug fixes for a few quality-of-life issues which were introduced in version RNAlysis

Stable release V3.5.1

3.5.1 (2023-02-22)

This version introduces minor bug fixes.

Fixed

• Fixed bug where the RNAlysis stand-alone app would sometimes fail to run CutAdapt (thanks to Matthias Wilm).
• Fixed bug where the User Guide action in the graphical interface would point to the Tutorial, and vice versa.
• The X and Y axis labels on volcano plots should now format the 'log' in the label correctly.

Stable release V3.5.0

3.5.0 (2023-02-08)

This version introduces new features such as differential expression analysis with the Limma-Voom pipeline,
customizable databases for the quick-search function, basic filtering and procrssing functions for gene sets,
improved progammatic API for FeatureSet and RankedSet objects, and RPKM and TPM read count normalization.
Several changes have been made to improve the user experience, including updated documentation,
improved clarity of function tooltips, clearer output formats, and faster download speeds for tutorial videos.

Added

• Added differential expression analysis with the Limma-Voom pipelines (CountFilter.differential_expression_limma_voom)
• You can now select which databases to display in the right-click quick-search menu, using the settings menu.
• Gene sets now support some basic operations (filtering, gene ID translating, etc) through the graphical interface.
• enrichment.FeatureSet and enrichment.RankedSet now support some filtering operations from the filtering module (such as filtering by user-defined attributes, GO terms, or KEGG pathways).
• Added reads-per-kilobase-million (RPKM) and transcripts-per-million (TPM) normalization methods (CountFilter.normalize_to_rpkm() and CountFilter.normalize_to_tpm()).

Changed

• Classes enrichment.FeatureSet and enrichment.RankedSet now inherit from Python base-class set, and can be interacted with like other Python sets. The old API and attributes of these classes were maintained as they were.
• Improved documentation for some functions.
• Function selection tooltips should now display information more clearly.
• Pipelines that contain consecutive clustering/splitting functions will now return their outputs in a clearer format.
• Enrichment bar-plots should now adjust the x-axis limits more tightly to fit the displayed data.
• Improved clarity of automatic titles in enrichment plots.
• Download/update speed of tutorial videos has improved significantly.

Fixed

• Fixed bug where Pipelines would not always properly run 'translate_gene_ids'

Stable release V3.4.2

3.4.2 (2023-02-01)

This version introduces minor bug fixes.

Fixed

• Fixed bug where updating RNAlysis through the graphical interface would not update some of the optional dependencies.
• Fixed typos in the documentation.

Stable release V3.4.0

3.4.0 (2023-02-01)

From this release forward, RNAlysis is made available as a stand-alone app for Windows and MacOS. You can download these stand-alone versions from the GitHub Releases page.
In addition, new features were added, including new plots, filtering functions, integration of the external tools bowtie2 and featureCounts, and the ability to generate Gene Ontology Graphs and KEGG Pathway Graphs without running enrichment analysis from scratch.

Added

• Added a Scree Plot (explained variance per PC) to Principle Component Analysis
• Added CountFilter.split_by_principal_component(), allowing users to filter genes based on their contributions (loadings) to PCA Principal Components.
• Added Filter.drop_columns
• Added support for the Sharpened Cosine distance metric in clustering analyses
• KEGG enrichment can now generate KEGG pathway graphs for pathways that were found to be statistically significant
• Added functions to the enrichment module that can generate KEGG Pathway or Gene Ontology plots based on previously-generated enrichment results
• You can now clear the RNAlysis cache from the RNAlysis GUI, or through the general module.
• Added bowtie2 alignment to the fastq module.
• Added FeatureCounts feature-counting to the fastq module.
• You can now choose whether or not to discard genes from enrichment analysis if they have no annotations associated with them.
• Added sections to the programmatic user guide about the fastq module.

Changed

• Replaced the 'parallel' parameter in enrichment functions with the 'parallel_backend' parameter, allowing users to choose which parallel backend (if any) will be used in the function.
• Added 'parallel_backend' parameter to all clustering functions under the filtering module.
• When generating Gene Ontology/KEGG Pathway graphs, users can choose whether or not to generate the figure in an additional separate file.
• Updated type annotations of some functions to be more precise and helpful (for example, setting a lower bound on some int function parameters).
• The colorbar ticks in enrichment bar plots now match the axis ticks on the main axis.
• Slight improvements in GUI performance, stability, and looks.
• Slight improvements in performance of enrichment analysis when examining a small number of attributes.
• enrichment.plot_enrichment() was replaced by enrichment.enrichment_bar_plot().
• CountFilter.differential_expression() has new optional parameter output_folder, which allows users to save the generated data tables and the R script that generated them into a specified folder.

Fixed

• In CountFilter.differential_expression_deseq2(), fixed a bug where design matrix files with non-comma delimiters would cause an error (thanks to Mintxoklet in #7)
• Fixed bug where setup.py would install a directory named tests into site-packages folder (thanks to Bipin Kumar in #9)
• Fixed bug where the windows of some functions (differential expression, adapter trimming, etc) did not show a link to the function's documentation page.
• Fixed typos in some parts of the RNAlysis documentation
• When filtering a table by a single user-defined attribute, the automatic table name will now be more informative about the operation applied.
• Fixed bug where occasionally a Pipeline or Function would generate multiple tables of the same name, but only one of them will appear in the GUI.
• Fixed bug where occasionally significance asterisks on enrichment bar-plots would appear in the wrong location.
• Fixed bug where fastq.create_kallisto_index() (Create Kallisto Index) would not make use of the make_unique parameter (thanks to Matthias Wilm)

Removed

• Removed the previously-deprecated functions enrichment.enrich_randomization() and enrichment.enrich_hypergeometric().

New Contributors

• [Mintxoklet] in [#7]
• [Bipin Kumar] in [#9]
• Matthias Wilm

Stable release 3.3.0

3.3.0 (2022-12-02)

• This version introduced quality-of-life improvements to the graphical user interface.

Added

• Added a Frequently Asked Questions page, and linked all RNAlysis help material inside the graphical interface Help menu.
• Pipelines can now be edited and deleted through the Pipeline menu of the graphical interface.
• Added Contributing page to the documentation, with basic guidelines on how you can contribute to the RNAlysis project!

Changed

• All open tabs are now always visible in the main menu screen. Tab names are now shortened with ellipsis if nessecary.
• The right-click context menu of the main menu tabs now allows users to open a new tab at a specific position, or close a specific tab/tabs to the right/tabs to the left/all other tabs.
• RNAlysis documentation is now split into GUI documentation (quick-start video guide, tutorial, GUI user guide), and programmatic documentation (programmatic user guide)
• Improved readability of RNAlysis logs
• Pipelines are now exported with additional metadata - the version of RNAlysis they were exported from, and the date and time it was exported. This metadata should not affect Pipelines that were created in older versions, and does not affect the way Pipelines are applied to data tables.

Fixed

• RNAlysis now warns users if they attempt to overwrite an existing Pipeline.
• Fixed an incorrect keyboard shortcut for Export Pipeline action