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NEWS.md

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jampack version 0.0.24.9000

  • updated dependencies:

    • farrisdata to 0.0.11.900

jampack version 0.0.23.9000

  • updated dependencies:

    • splicejam to 0.0.81.900

      • fix error "width() not found"
      • silence the warning that shinyWidgets::setShadow() is deprecated
      • added Troubleshooting to launchSashimiApp() for web connection errors.

jampack version 0.0.22.9000

  • updated dependencies:

    • splicejam to 0.0.80.900
    • jamba to 0.0.102.900
    • colorjam to 0.0.28.900
    • jamma to 0.0.33.900
    • farrisdata 0.0.10.900 (optional)
    • ComplexHeatmap to 2.15.4 (optional)

  • Holding off for now about requiring R-4.0.0, although it might be necessary in future.

  • In future, all Depends may move to Imports, so that packages will need to be loaded properly rather than being loaded via jampack itself. Unclear.

jampack version 0.0.21.9000

updated dependencies on splicejam to 0.0.75.900

changes

  • Edits to README.md and farrisSeq.Rmd to include link to the paper in Cell Reports.

jampack version 0.0.20.9000

changes

  • farrisSeq.Rmd was updated to include links to GEO, and to re-word several paragraphs to match updated figure numbering.

jampack version 0.0.19.9000

changes

  • farrisSeq.Rmd was updated to include Sashimi plots via the "splicejam" package. Also, description of MultiEnrichMap methods were included, referencing the "multienrichjam" R package.

jampack version 0.0.18.9000

changes

  • Updated DESCRIPTION with higher required package version numbers for jamba, splicejam, jamma, colorjam, to force updates for those packages as needed.

jampack version 0.0.17.9000

changes

  • farrisSeq.Rmd was updated to include prefixes for tidyselect functions, including tidyselect::ends_with(), tidyselect::contains(), and tidyselect::matches(). Also added tidyselect to packages loaded at the start of the Rmd.
  • Added dplyr and tidyselect to "Suggests:" in the DESCRIPTION file, as they are required by farrisSeq.Rmd` but not required otherwise.

jampack version 0.0.16.9000

changes

  • splicejam::defineDetectedTx() was updated to allow conversion of zero expression values to NA, slightly improving the accuracy of transcript group mean expression values, which is the new default. For consistency, zeroAsNA=FALSE was added to farrisSeq.html to ensure consistency with previous calculations.
  • Updated the README.md page to include direct links to the online documentation for each Jam R package.
  • Reduced the number of files included in the R package build.

jampack version 0.0.15.9000

changes

  • Updated farrisSeq.Rmd to use prefixed ComplexHeatmap::draw() instead of draw() because of R method dispatch errors when another package is loaded that defines a generic draw() function.
  • Also confirmed that ComplexHeatmap requires the Github version, which provides Heatmap() arguments such as left_annotation. It should be available on Bioconductor after the next Bioconductor release (as of April 21, 2019.)

jampack version 0.0.14.9000

  • Export per-gene isoform summary statistics to Excel xlsx files, with each contrast in its own worksheet. Requires jamba (>= 0.0.29.900).
  • Fixed issue where numTx was not reported from runDiffSplice(), resolved in splicejam (>= 0.0.14.900). Updated DESCRIPTION to add this version requirement.

jampack version 0.0.13.9000

  • Differential isoform analysis, experiment design and contrast definitions added to Rmarkdown.

jampack version 0.0.12.9000

  • ALE violin plot implemented, requires splicejam v0.0.11.900 or higher.

jampack version 0.0.11.9000

  • Further ALE analysis steps.

jampack version 0.0.10.9000

  • Added section for ALE processing, and comparison of proximal to distal ALE regions.

jampack version 0.0.9.9000

  • Requires splicejam 0.0.26.900 for several new functions.
  • Added methods for ALE for proximal-distal ALE analysis.

jampack version 0.0.8.9000

  • Moved "library()" calls to the Rmarkdown body, they should be displayed in the HTML output so others can copy-paste them to test the R code.

jampack version 0.0.7.9000

  • Added stacked bar chart for transcript types by Neuronal Transcript List.
  • Created "detected" Neuronal Transcript Lists, which is used to describe the transcript types.
  • Modified detectedTxTPManyL to use CB and DE samples, as was done originally and in the manuscript.
  • Enhanced the heatmap of Neuronal Transcripts, using newer options in ComplexHeatmap on Github which are not yet on Bioconductor. Depends was updated to point to Github, will be changed to Bioconductor once it is released there.
  • Added rmarkdown to Suggested packages, since it is required to render the farrisSeq.Rmd file.
  • Added instructions for building the farrisSeq.Rmd HTML report.
  • Removed liao_style.css which was mostly useful for customized table rendering, and is not necessary for this Rmarkdown file.
  • Incremented some required version numbers for other Jam packages.

jampack version 0.0.6.9000

  • Added Rmarkdown cache.extra to the "docs/farrisSeq.Rmd" file, dependent upon package versions of "farrisdata" (in the event the source data changes), and "splicejam", "jamba" (packages which provide some key data manipulation functions.)
  • Added transcript type definitions per transcript list.
  • Added Suggests for "png" and "Cairo" packages, which should help with ComplexHeatmap.
  • Added colorSub section to the visible Rmarkdown body, previously it was in the header but was not visible, therefore making it difficult to reproduce the workflow by copy-pasting from the rendered HTML code blocks.
  • Added specific R package versions to the DESCRIPTION, to ensure jampack will require important versioned changes in Jam packages as needed.

jampack version 0.0.5.9000

  • Added specific sections for supplemental figure 7, for each panel.
  • Added heatmap of expression data using ComplexHeatmap instead of heatmap.3(). Will assess adding text labels onto the color bars beside and at the top of the plot.

jampack version 0.0.4.9000

  • Updated README.md with more specific instructions on installing jampack and farrisdata, in order to reproduce the Rmarkdown HTML output.
  • Fixed typo in the description of Gene data matrix, which represents Salmon pseudocounts and not TPM values.

jampack version 0.0.3.9000

changes to package dependencies

  • farrisdata and seqinr were added to Suggests, since they are required for building the docs/farrisSeq.Rmd but are otherwise not required for the package.
  • Added 3 prime UTR length and CAI analysis sections, along with support functions updated in splicejam.