Changes in version 1.2.7 (2023-04-06)
This major update brings GRaNIE in this release branch of Bioconductor
to the latest version from the devel branch (1.3.34) before the code
freeze for Bioconductor 3.16. Because of the heavy development for the
GRaNIE package, we decided to provide the latest version also for
Bioc 3.16 for people who do not immediately update to Bioc 3.17.
For a full changelog, see the GRaNIE webpage.
Changes in version 1.2.4 (2023-01-31)
Bug fix
- due an external change at UCSC, forced to require at least version
1.34.8 of the GenomeInfoDb dependency. For more information, see
here. Otherwise, GenomeInfoDb::getChromInfoFromUCSC("hg38") returns
an error.
Changes in version 1.2.2 (2022-12-22)
Bug fix
- bug fix in plotCommunitiesEnrichment that was caused by the
tidyverse 1.2.0 related changes
Minor changes
- further small code changes related to tidyverse 1.2.0 changes
Changes in version 1.2.1 (2022-12-16)
- updated the package to devel version 1.3.11 due to many small
improvements, bug fixes, necessary changes etc
Changes in version 1.1.21 (2022-11-13)
Major changes
- major object changes and optimizations, particularly related to
storing the count matrices in an optimized and simpler format. In
short, the count matrices are now stored either as normal or sparse
matrices, depending on the amount of zeros present. In addition,
only the counts after normalization are saved, the raw counts before
applying normalization are not stored anymore. If no normalization
is wished by the user, as before, the "normalized" counts are equal
to the raw counts. GRaNIE is now more readily applicable for larger
analyses and single-cell analysis even though we just started
actively optimizing for it, so we cannot yet recommend applying our
framework in a single-cell manner. Older GRN objects are
automatically changed internally when executing the major functions
upon the first invocation.
- various Documentation and R help updates
- the function generateStatsSummary now doesnt alter the stored
filtered connections in the object anymore. This makes its usage
more intuitive and it can be used anywhere in the workflow.
- removed redundant biomaRt calls in the code. This saves time and
makes the code less vulnerable to timeout issues caused by remote
services
- due to the changes described above, the function plotPCA_all now can
only plot the normalized counts and not the raw counts anymore
(except when no normalization is wanted)
- the GO enrichments are now also storing, for each GO term, the
ENSEMBL IDs of the genes that were found in the foreground. This
facilitates further exploration of the enrichment results.
Minor changes
- many small changes in the code
Changes in version 1.1.13 (2022-09-13)
Major changes
- many Documentation and R help updates, the Package Details Vignette
is online
- The workflow vignette is now improved: better figure resolution,
figure aspect ratios are optimized, and a few other changes
- the eGRN graph structure as built by build_eGRN_graph() in the
GRaNIE object is now reset whenever the function
filterGRNAndConnectGenes() is successfully executed to make sure
that enrichment functions etc are not using an outdated graph
structure.
- the landing page of the website has been extended and overhauled
- removed some dependency packages and moved others into Suggests to
lower the installation burden of the package. In addition, removed
topGO from the Depends section (now in Suggests) and removed
tidyverse altogether (before in Depends). Detailed explanations when
and how the packages listed under Suggests are needed can now be
found in the new Package Details Vignette and are clearly given to
the user when executing the respective functions
- major updates to the function getGRNConnections, which now has more
arguments allowing a more fine-tuned and rich retrieval of eGRN
connections, features and feature metadata
- a new function add_featureVariation to quantify and interpret
multiple sources of biological and technical variation for features
(TFs, peaks, and genes) in a GRN object, see the R help for more
information
- filterGRNAndConnectGenes now doesnt include feature metadata columns
to save space in the result data frame that is created. The help has
been updated to make clear that getGRNConnections includes these
features now.
Minor changes
- small changes in the GRN object structure, moved
GRN@data$TFs@translationTable to GRN@annotation@TFs. All exported
functions run automatically a small helper function to make this
change for any GRN object automatically to adapt to the new
structure
- many small changes in the code, updated argument checking, and
preparing rigorous unit test inclusion
- internally renaming the (recently changed / renamed) gene type
lncRNA from biomaRt to lincRNA to be compatible with older versions
of GRaNIE
Changes in version 1.1 (2022-05-31)
Minor changes
- added the argument maxWidth_nchar_plot to all functions that plot
enrichments, and changed the default from 100 to 50.
Bug fixes
- fixed a small bug that resulted in the enrichment plots to ignore
the value of maxWidth_nchar_plot
Changes in version 0.99 (2022-04-26)
Major changes
- Bioconductor acceptance: this version is the final version for the
Bioconductor 3.15 release branch
- full inclusion of the GRN visualization
- extensive vignette updates
- added the possibility to print only particular output pages for all
plot functions
Bug fixes
- various minor bug fixes
Minor changes
- various minor changes
Changes in version 0.15-0.17 (2021-12-13)
Major changes
- all enrichment analyses have been extended and improved, we added
additional ontologies (KEGG, DO, and Reactome), more information in
the resulting summary plots
- all plotting functions have been homogenized and extended, PDF width
and height can now be set for all exported plot functions. Also, the
possibility to not to a PDF but instead to the currently active
graphics device is possible. Lastly, setting a different filename is
finally possible. Collectively, this provides ultimate flexibility
for customizing file names, the output devices used and PDF sizes
- we added a function to build the eGRN network that can be
parameterized and that allows future developmemt more easily. Now,
network-specific parameters can be changed, such as whether loops
should be allowed
- we removed the GRaNIEdev package, the development now happens in a
separate branch rather than a different package
- we added Leiden clustering for community clustering (see
https://www.nature.com/articles/s41598-019-41695-z for a comparison
with louvain)
- extensive vignette updates
Bug fixes
- various minor bug fixes
Minor changes
- changed the object structure slightly (graph slot and structure
within the stats$enrichment slot)
Changes in version 0.9-0.14 (2021-12-13)
Major changes
- major overhaul and continuous work on peak-gene QC plots
- the filterData functions has now more filter parameters, such as
filtering for CV. Also, all filters uniformly have a min and max
filter.
- integrated network statistics and various enrichment analyses
- handling of edge cases and rare events in various functions
- packages have been renamed to GRaNIE as basename (before: GRN)
Bug fixes
- various minor bug fixes
Minor changes
- changed the object structure slightly and moved some gene and peak
annotation data (such as mean, CV) to the appropriate annotation
slot
Changes in version 0.8 (2021-05-07)
Major changes
- improved PCA plotting, PCA plots are now produced for both raw and
normalized data
- new filters for the function filterGRaNIEAndConnectGenes
(peak_gene.maxDistance) as well as more flexibility how to adjust
the peak-gene raw p-values for multiple testing (including the
possibility to use IHW - experimental)
- new function plotDiagnosticPlots_TFPeaks for plotting (this function
was previously called only internally, but is now properly
exported), in analogy to plotDiagnosticPlots_peakGene
Bug fixes
- various minor bug fixes (PCA plotting, compatibility when providing
pre-normalized data)
Minor changes
- changed the object structure slightly and cleaned the config slot,
for example
- some functions have been added / renamed to make the workflow more
clear and streamlined, see Vignette for details
- some default parameters changed
Changes in version 0.7 (2021-03-12)
Major changes
- improved PCA plotting, also works for pre-normalized counts now when
provided as input originally
- more flexibility for data normalization
- homogenized wordings, function calls and workflow clarity, removed
unnecessary warnings when plotting peak-gene diagnostic plots, added
more R help documentation
- added IHW (Independent Hypothesis Weighting) as a multiple testing
procedure for peak-gene p-values in addition to now allowing all
methods that are supported by p.adjust
Bug fixes
- various minor bug fixes
Minor changes
Changes in version 0.6 (2021-02-09)
Major changes
- significant speed improvements for the peak-FDR calculations and
subsequent plotting
- TF-peak diagnostic plots now also show negatively correlated TF-peak
statistics irrespective of whether they have been filtered out in
the object / pipeline. This may be useful for diagnostic purposes to
check whether excluding them is a sensible choice and to confirm the
numbers are low
Bug fixes
- Numbers for connections per correlation bin in the TF-peak
diagnostic plots were wrong as they did not correctly differentiate
between the different connection types in case multiple ones had
been specified (e.g., expression and TF activity). This has been
fixed.
Minor changes
Changes in version 0.5 (2021-02-02)
first published package version