@s-andrews s-andrews released this Sep 17, 2018 · 3 commits to master since this release

Assets 2


This release was an opportunity for a general cleanup of a lot of cosmetic
issues which had been building up, as well as addressing a number of bugs.

Things which we fixed were:

  • Fixed the text alignment on a lot of plot axes to be more pretty

  • Fixed a data scaling bug on the QQ plot which sometimes missed out the
    last point

  • Fixed a crash in LIMMA when data contained NA values

  • Fixed a cancellation bug in the HiC heatmap

  • Fixed a null pointer bug in the proportion of library bug

  • Added an option to save the data from the quantitation trend plot

  • Added whitespace support to generic text import

  • We now record the import options used when importing data

  • Handle platforms where we can't automatically open a web browser better

  • Fixed a bug where the read position probe generator only did a single chromosome

  • Improved the layout of the quantitation trend heatmap

  • Fixed a bug with NA or infinite values in the quantitation trend plot

@s-andrews s-andrews released this Jun 6, 2018 · 65 commits to master since this release

Assets 2


This release has a fix for a potentially nasty data import bug introduced in
v1.40.1 and adds some new visualisation features.

Important Data Import Bug

We are indebted to John Chuang for spotting a data import bug which was
introduced in v1.40.1 and which could corrupt data imported from sorted
BAM files containing duplicated sequences. We'll do a full write up
elsewhere but the details of the bug can be seen in:


In short, if you have imported a sorted BAM file using SeqMonk v1.40.1 or
v1.41.0 then you may have had some duplicate reads silently discarded. The
issue could also theoretically affect sorted files, but the number of
sequences affected would be extremely low and is unlikely to materially
affect any datasets.

Projects which had data imported in an earlier version of seqmonk, and the
project was opened and saved in the affected versions are not affected.
The bug is in the import step.

If you imported sorted files into an affected version of the program then
we recommend that you create a new project and re-import the BAM files
using seqmonk v1.42.0 (or later).

Other changes in this release:

  • Added a size factor normalisation quantitation

  • Fixed a data update bug when creating custom genomes

  • Added a new Quantitation Trend Heatmap plot, and optimised the old
    Quantitation Trend Plot code

  • Worked around an EdgeR installation bug which caused the EdgeR
    filter to break.

  • Fixed a problem with the linux themeing on Ubuntu 18.04

@s-andrews s-andrews released this Apr 3, 2018 · 119 commits to master since this release

Assets 2

This release adds some new functionality, but also tidies up a lot of existing
features, making them work more smoothly.

  • Added a QQ plot

  • Improved the options and multiple testing correction in the logistic
    regression filter.

  • Fixed a slowness issue when working with hundreds of samples.

  • Added a mechanism to allow projects to update to newer versions of
    core annotations in the same assembly.

  • Added a fix for the RNA-Seq QC plot when there isn't a rRNA track in
    the annotation.

  • Modified the DESeq filter to allow multiple group comparisons by using
    the Likelihood ratio test.

  • Report the parameters estimated by the RNA-Seq pipeline.

@s-andrews s-andrews released this Feb 21, 2018 · 169 commits to master since this release

Assets 2

This is a bugfix release of seqmonk which adds some optimisations to the
background data model and fixes a number of bugs.

  • Changed the internal data model to store positions and counts separately
    to make the storage of heavily duplicated data much more efficient

  • Added a LIMMA statistical filter

  • Modified the GTF parser to better deal with the structure of Ensembl
    GTF files.

  • Changed all of the launchers so you can pass a file name to open. Allows
    file extensions to be associated with seqmonk so you can open projects
    by double clicking on them.

  • Improve the merging of transcripts in the RNA-Seq pipeline to use
    gene ids where they are present in the annotation so we don't get
    spurious merging of overlapping transcripts on the same strand which
    are annotated as belonging to different genes.

  • Updated the genome processing scripts so that gene_ids are added to
    all transcripts

  • Fixed a crash in the aligned probes plot when no data stores are visible

  • Fixed a display bug for the list of features in the feature filter and
    quantitation trend plot.

  • Fixed an inefficient packing algorithm when the number of reads was too
    great to be displayed within the available height of the chromosome view.

@s-andrews s-andrews released this Jan 2, 2018 · 209 commits to master since this release

Assets 2


This release does some major reorganisation of the filtering menu as well as
adding new functionality. Major changes are:

  • Completely restructured the statistics filter menus so that they are
    now arranged by the type of data they apply to.

  • Added an option to detect and remove duplication in the RNA-Seq
    quantitation pipeline.

  • Added a new variant of the EdgeR filter which can work on for/rev
    ratio data such as methylation data.

  • Added an option to change the startup memory settings from the usual
    preferences dialog.

  • Added an R debug mode to make it easier to track down problems with R
    based functionality.

  • Fixed a bug in the variation plot for data containing NaN values

  • Fixed a regression which meant some functionality didn't work on systems
    running java 1.6

  • Added an option to create data groups or replicate sets from pre-prepared
    lists of data store names.

  • Added a global correction to the aligned probes plot to make the plots
    more directly comparable.

  • Fixed a bug in the exporting of images from the aligned probes plot.

  • Collated error messages to help interpreting large numbers of errors.

  • Added a strand bias plot

@s-andrews s-andrews released this Nov 6, 2017 · 247 commits to master since this release

Assets 2

This release is a mix of new features and bug and usability fixes for existing
features. Major changes are:

  • Added the ability to have multiple annotation versions for the same genome
    assembly release. We needed a way to update the annotations used for some of
    the major eukaryotic genomes, when the sequence level assembly hadn't actually
    changed. All genomes can now have multiple versions distinguished by the Ensembl
    release number from which they came. The genome selection interface now shows
    the different annotation versions for the same genome assembly grouped together.

  • Added a parser for the BEDPE file format

  • Added a better filtering for absolute change to the binomial, chi-square and
    logistic regression filters.

  • The hierarchical cluster plot now allows for the highlighting of replicate sets
    at the top.

  • The gene set filter now provides the option to use the Kolmogorov-Smirnov test
    as well as the t-test when finding changing gene sets

  • Altered the feature filter to allow it to simultaneously use multiple feature tracks

  • Improved the scaling of the aligned probes plot so that the absolute numbers reported
    are more meaningful

  • Added a scale bar to the aligned probes plot

  • Fixed a crash in the PCA plot when no data remained after removing null values

  • Fixed a crash when saving results from the correlation matrix

  • Fixed a bug which allowed replicate sets to be added to other replicate sets
    when auto-creating sets in the data store tree

@s-andrews s-andrews released this Jun 20, 2017 · 294 commits to master since this release

Assets 2

This is a bugfix release which mainly addresses a bug in the most recent
jave release on OSX. Specific changes in this release are:

  • Fixed a hang bug specifically triggered in java v1.8_131 when creating
    any report. The bug doesn't affect other platforms, or previous versions
    of the JRE.

  • Fixed a problem with the auto-setup of the perplexity setting in the Tsne
    plot which affected projects with fewer than 7 samnples.

  • Fixed a bug which caused the intensity gene set plot to not clean up
    temporary probe lists when the list of hits was sorted.

@s-andrews s-andrews released this Jun 6, 2017 · 303 commits to master since this release

Assets 2

This is a bugfix release which addresses some issues found in the previous
release. Specifically

  • We fixed a performance bug when creating custom genomes from fasta or gff
    files with very large numbers of sequences in them. This would have affected
    people building custom genomes from very fragmented sets of contigs.

  • We added a scale bar to the HiC heatmap

  • We changed the TSNE code to use Rtnse instead of tsne to work round a bug and
    to improve performance

  • We added some more debugging output to the launch script to make it easier to
    debug launching problems

  • We fixed a bug in the SplicingEfficiency pipeline affecting genomes with
    non-Ensembl naming schemes

  • We fixed a bug in PCA plotting when showing labels in plots with overlapping

@s-andrews s-andrews released this May 19, 2017 · 319 commits to master since this release

Assets 2

This release adds some new plotting options for data store similarity and greatly improves the workflow for the analysis of splicing as well as adding some more general bug fixes and improvements.

Major changes are:

  • Added a TSNE plot for clustering data stores

  • Added colouring to the correlation matrix

  • Added a logistic regression splicing statistical filter

  • Greatly improved the efficiency of the exactly overlap quantitation

  • Added strand information to probe reports

  • Fixed a bug in the launcher for UTF8 locales

  • Fixed a bug in the normalisation of paired end RNA-Seq data

  • Fixed a crash in bioconductor installation

@s-andrews s-andrews released this Jan 30, 2017 · 375 commits to master since this release

Assets 2


This release is a minor bugfix release. Updating to this release is only
necessary for people directly affected by one of the bugs below:

  • Fixed a bug in the reporting of R errors where the full R trace wasn't
    attached to the crash report making it difficult to identify the cause
    of R problems.
  • Fixed a bug in the generation of custom genomes where feature names
    containing a forward slash in their names would cause a failure of the
    feature caching system.
  • Fixed an out of date warning in the RNA-Seq pipeline which hadn't been
    updated to the new option names in the BAM import dialog.