Changelog
Source:NEWS.md
Version 1.11.0
Minor Changes
- Sorted differential plots - can use a ‘sort’ aes in plot-profiles. If it matches a column in results, differential heatmaps are sorted accordingly. If it’s prefixed with a ‘+’, then the tree branches are sorted accordingly.
- Better contrast naming
- Differential heatmaps are feature-clustered based only on the ‘involved’ samples (which now falls back to the ‘influential’ samples when auto-involvement isn’t calculated. # Version 1.10.0 ## Major Changes
- Change default fastq.gz location prefix to
inputs/sequencing/data, rather thaninputs/sequencing/released - Allow abbreviated spec files, from verbose
sample_set(models=list(model(...), model(...))tosample_set(model(...), model(...))## Minor Changes - chore: Bring in the updated environment/docker infrastructure
- chore: Tidy up the load_specs
- feat: First stage of switching profile_plot and comparison to standard wrap
- feat: Add mcols to xl files
- feat: Add dendrogram row-cluster splits
- fix: Ensure the spec’s evaluated/unevaluated objects stay in sync
- feat: Allow custom fastq dirs
- fix: Change where we look for fastq files
- fix: Ensure children of profile_plots and comparisons are valid
- docs: Update pkgdown handler # Version 1.9.0 ## Major Changes ## Minor Changes
- Throw error when no config files found
- Add ability to distribute shiny apps as resources
- Refactor heatmap plotter
- Better shiny-explorer. Update to latest template.
- feat: Generate release notes
- fix: Remove single quotes from comparison names
- fix: Ensure plotting dds is refreshed each model
- feat: robust retag
- chore: Cleaner wrapping of make targets in sbatch/container
- feat: Add table to track impact of feature-filtering
- style: Trim down excess menu levels from sidebar
- style: Improve figure legends
- docs: Document the new specfile additions # Version 1.6.1
Major Changes
- Use
extra_assaysin differential plots - Allow stratified normalisation
- add
make retagto allow versions to be added post-run
Minor Changes
- Refactor partials for elegance. Add masks - na assays
- Fix masks breaking plots that don’t know about them
- Improve clustering
- Latest infrastructure - late-expanded HOME
- Fix differential heatmaps
- Add retagging
- Add alternative assays to the differential analysis
- Improve scaling/centring in differential plots
- Update documentation with recent additions
Version 1.4.0
Version 1.3.0
Major Changes
- Improve plots by z-scoring
- Improve the merge_yml functionality
- Reimplement partials for speed
Minor Changes
- Improve documentation procedure
- Bring tabs to the exploratory page
- Improve the page resize toggle
- Add lightbox
- Add env files back in
- Remove some unneeded functions
- Tidy up roxygen tags
- Start the model-constraint handler
- Better handling of env-vars with spaces, eg fullname
- Refactor for author roles, and move meta to the _quarto.yml
- Delegate differential module to separate template
- Auto-generate the secret and shared mks from the central differential one
- Partial implementation of model constraints
- Work-around for an R bug
- Don’t over-write the ‘design’ function with a variable.
- Fix typo
- Add facet wrapper
- Better handling of org packages
- Tidy up git inclusion
Version 1.2.0
Major Changes
- Rearrange report sections to put all plots related to a mode/comparison in the same section
- Introduce interactive plots
- Include the ‘influential_samples’ functionality
- Output estimated means in supplementary csv’s
Minor Changes
- Update launchers (indentation)
- Use the .env that specifies the R docker/singularity images
- Update infrastructure to v1.2.0 - more/all settings in .env
- ssh_auth_sock
- Fix missing vars in env
- Sync with launcher 1.2.2
- Fix SSH_AUTH_SOCK needing to be set
- Fix singularity missing from nfcore module
- Prep for big import of changes
- New data-model-profile=type hierarchy
- Improve categories - probably broken the sidebar though
- Bring in new template. Deloop differential partially
Version 1.0.0
Major Changes
- Add differential_subsets functionality
- Update to v1.0.1 of generic template
- Slurm refactor - ‘make sbatch run’ instead of ‘make run SUBMIT=true’
Minor Changes
- Ensure percentNA is available where applicable
- Add custom alpha for profile plots
- Ensure non-estimable ‘fully missing’ coefs aren’t calculated
- Minor changes
- Fix the alpha_scale lack of self-reflection
- Add omnibus for limma
- Update to latest launchers
- remove qc_formulae
- Update launchers. Fix edge-cases in pipeline
- Fix renv calling
- Document the differential_subset setting
- Update pkgdown generation
Version 0.23.0
Major Changes
- Add ability to take on summarizedexperiments
- Update ‘differential heatmap baseline’ method so that it uses emmeans modifications to work directly with constituent factors and their levels
- Remove site Renviron. Users must now set
SINGULARITYENV_RENV_PATHS_{LIBRARY,ROOT,PREFIX_AUTO}in their bashrc file
Version 0.20.0
Version 0.18.0
Version 0.14.0
Version 0.13.0
Version 0.12.0
Version 0.11.1
Major Changes
-
make R-localnow produces a file e.g. R-4.3.2 that by doesn’t include any additional bindings or environment variables within the container - people are increasingly putting settings in theHOMEarea that broke containment when running interactively. Instead, if you want to include extra access, set the variableINTERACTIVE_SINGULARITYin your~/.bashrce.g.export INTERACTIVE_SINGULARITY='--bind $$HOME/.Xauthority,$$HOME/.Xdefaults,$$HOME/.Xresources,$$HOME/.emacs.d,$$HOME/.ssh --env DISPLAY=$$DISPLAY'. The double$means that those variables will get expanded at runtime, rather than at the point you generateR-4.3.2(which would mean thatDISPLAYwould be out of date).
Version 0.11.0
Major Changes
- Change the way version numbers are propagated to the quarto report - the qmd files don’t get tagged now (to allow better cacheing - not yet implemented), but instead the figures get the git information inserted into their filenames.
- Rationalise the directory structure -
resourcesnow contains the auxilliary makefiles and the renv initialisation files. And extra files either from other modules (such as the spec files and configs) get put intoextdataalong with things likeR.bib