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@s-andrews s-andrews released this 08 Jun 09:58
· 66 commits to master since this release
v1.47.0
b069f73

This version introduces some major changes for users of Mac OSX
and improves a lot of existing functionality.

There are two major changes of note:

  1. The way the OSX package is built has been changed so that we can
    deal with the new security model in OSX v10.15 (Catalina). People
    working on that version will have found that they were unable to
    load or save data to anywhere other than their home directory.
    This new version now tests for limited disk access on OSX and if
    it finds it it will point to instructions for how SeqMonk can be
    given more generous permissions to read data from places like USB
    drives, network shares and the Desktop.

  2. We've made a relatively minor change to the way that RNA-Seq
    quantitation works. When we merge transcript isoforms we used to
    prefer matching transcripts based on them having compatible names
    (eg ABC-201 would merge with ABC-202), and based on them actually
    overlapping in the genome. We found though that some gene models
    from Ensembl broke these assumptions (ie there are cases with
    two different genes with identical names which overlap, and cases
    of genes with multiple transcripts which don't overlap). These
    cases are all nuts but they exist so we need to deal with them. We've
    now changed to prefer using the "gene_id" annotation on transcripts
    to decide which ones to merge, which deals better with these edge
    cases. What this means though is that if you have an existing
    RNA-Seq analysis in a project and you re-quantitate it having moved
    to the new SeqMonk version that your probe set will be replaced as
    it won't match the exsting set because of these changes. You will
    therefore need to either re-create your filtered lists using the
    new probe set - or stick to an older version of SeqMonk to finish
    off those existing projects.

Other more minor changes are:

  1. Improve the default matching options and save name for annotated
    probe reports.

  2. Added a vistory event for adding annotation

  3. Added replicate set colouring to boxplots and beanplots

  4. Made the default heatmap colours more friendly to colourblind people

  5. Changed the min R version to 3.6 as Bioconductor is broken for
    versions older than that.

  6. Fixed a StarWars layout bug for multiple lists and one store.

  7. Use https to communicate with web services

  8. Try to improve R package installs on OSX

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