Changes in version 1.7.3-1.7.4 (2024-04-03)
New features
- We offer an exciting new feature: Integrating Capture Hi-C or more
generally known promoter-enhancer interactions directly into the
GRaNIE framework to complement / guide the peak-gene search. For
more information, see the Package vignette and the R help for
addConnections_peak_gene().
- Added support for the new JASPAR2024 package and TF motives.
Bug fixes
- small bug fixes
Changes in version 1.7.2 (2023-12-08)
Improvements
- plotPCA_all() now also stores all screeplot and PCA results in the
object within GRN@stats$PCA
Changes in version 1.7.1 (2023-10-26)
- version jump due to new Bioconductor development cycle
Bug fixes
- fixed an accidentally recently introduced bug that caused an error
in addTFBS when using the JASPAR database
- made the code more error prone related to AnnotationHub and caching
annotation data in cases when the cache directory is corrupted or
deleted
Changes in version 1.5.4 (2023-09-11)
Workflow changes
- we modified the function filterData for cases when too few peaks
survive the filtering. Before, the function threw an error when the
number of peaks left was < 1000. Due to the error, the original GRN
object was not updated in such a case and one could accidentally
continue with the normal workflow because the GRN object before the
filtering would be taken as input instead for subsequent functions.
Now, only a warning is produced.
Changes in version 1.5.2-1.5.3 (2023-08-20)
New features
- say hello to a new function filterConnectionsForPlotting() that can
be used to include or exclude particular connections from the stored
eGRN for visualization purposes only (!). Note that this filter only
applies to visualization and enables a flexible system to visually
explore particular features of the stored eGRN. This is particularly
handy when the eGRN is large. For more details, see the help pages
of the new function.
- similarly, the function visualizeGRN() now by default only
visualizes connections that are marked as such (the result from
filterConnectionsForPlotting()) - that is, it excludes connections
that the user beforehand excluded from plotting. This allows to
specifically plot only part of the eGRN network and explore specific
T&F regulons, for example, a feature that before was not so easy to
do.
- It is now possible to integrate SNP data into GRaNIE via the new
function addSNPData(). For more information, see the Package
vignette.
Changes in version 1.5.1 (2023-06-19)
- version jump due to new Bioconductor development cycle
New features and stability improvements
- we replaced biomaRt for the full genome annotation retrieval in
addData with a different approach that is more reliable, as we had
more and more issues with biomaRt in the recent past. While using
the old biomaRt approach is still an option, the default is now to
use the AnnotationHub package from Bioconductor. This makes GRaNIE
overall more stable and less reliant on biomaRt due to the strict
timeouts and query size restrictions.
Changes in version 1.3.36 (2023-05-09)
New features and vignette updates
- a new correlation method has been implemented that replaces the
"old" robust method (via addRobustRegression) that was available as
an experimental feature until now. It is implemented in the WGCNA
package and called biweight midcorrelation or short bicor, a robust
type of correlation based on medians that can be used as an
alternative to Spearman correlation. Biweight midcorrelation has
been shown to be more robust in evaluating similarity in gene
expression networks and is often used for weighted correlation
network analysis. In addition, this new correlation type can now
also be selected for the TF-peak correlations, which was not
possible before. Lastly, the code has been cleaned and simplified
and all instances of addRobustRegression have been removed and
replaced by a new third option bicor (in addition to Pearson and
Spearman, as before) for the corMethod argument in multiple
functions that support this feature. All vignettes have been updated
accordingly.
- in addData, when a DESeq2 size factor normalization is selected by
the user, it is now explicitly checked whether enough genes are
available that contain no 0 values on which the size factor
normalization is based on. If this is not the case (the default and
hard-coded limit is currently set to a minimum of 100), an error is
thrown. This becomes particularly relevant for single-cell derived
data with a high fraction of 0s, and prevents a normalization based
on very few genes and improves the error messages that DESeq2 throws
otherwise for an improved user experience.
Changes in version 1.3.35 (2023-05-08)
Bugfixes and stability improvements
- improved the stability of the biomaRt call, which did not work as
originally intended in case of temporary connection failures. Now,
calls to biomaRt are attempted up to 40 times to increase the
chances of not suffering from connection issues. Also, the approach
to deal with BiocParallel failures has been changed.
Paper acceptance and publication update
- We are particularly excited to announce that the GRaNIE and GRaNPA
paper is finally out! See here for the final article in Molecular
Systems Biology.
Changes in version 1.3.34 (2023-03-29)
Bugfixes
- many small bugfixes and other small improvements to homogenize the
user experience due to the usage of systematic unit tests
Changes in version 1.3.33 (2023-03-06)
New features and vignette updates
- we provide two new functions with this update:
1. getGRNSummary() that summarizes a GRN object and returns a named
list, which can be used to compare different GRN objects ore
easily among each other, for example.
2. plotCorrelations() for scatter plots of the underlying data for
either TF-peak, peak-gene or TF-gene pairs. This can be useful
to visualize specific TF-peak, peak-gene or TF-gene pairs to
investigate the underlying data and to judge the reasonability
of the inferred connection.
- methods vignette updates
Changes in version 1.3.31-1.3.32 (2023-03-06)
Bugfixes
- various small bugfixes that were accidentally introduced in the
latest change from using the TF.ID instead of TF.name column as
unique TF identifier
Changes in version 1.3.26-1.3.30 (2023-03-06)
New features and vignette updates
- added two new supported genomes: rn6/rn7 and dm6 for the rat and the
Drosophila (fruit fly) genome, respectively
- added preliminary support for a new, alternative way of how to
import TF and TFBS data into GRaNIE. We now additionally offer a
more user-friendly way by making it possible to directly use the
JASPAR2022 database. You do not need any custom files anymore for
this approach! See the Package vignette for more details.
Bugfixes
- fixed a regression bug in addConnections_TF_peak (Column
peak.GC.class doesn't exist.) that was caused due to the recent GC
modifications
Changes in version 1.3.25 (2023-02-20)
New features and vignette updates
- additional significant methods vignette updates
- updates and clarifications for the workflow vignette
- a new QC plot for plotDiagnosticPlots_TFPeaks (and indirectly in
addConnections_TF_peak when plotDiagnosticPlots = TRUE) on page 1
that shows the total number of connections for real and background
TF-peak links as calculated and stored in the GRN object, stratified
by TF-peak FDR and correlation bin. This is a similar plot as we
show in the paper and helps comparing foreground and background.
Improvements
- speed improvements for plotDiagnosticPlots_TFPeaks (and indirectly
in addConnections_TF_peak when plotDiagnosticPlots = TRUE) when
plotAsPDF = FALSE
Bugfixes
- fixed a bug that only occurred in addConnections_TF_peak when using
useGCCorrection = TRUE
Changes in version 1.3.24 (2023-02-20)
New features and vignette updates
- significant methods vignette updates that help clarifying methods
details
Changes in version 1.3.22-1.3.23 (2023-02-15)
Minor changes
- Small workflow vignette updates
Bug fixes
- we were informed that newer versions of dplyr (1.1.0) changed their
default behavior for the function if_else when NULL is involved,
which caused an error. We changed the implementation to accommodate
for that and now avoid dplyr::if_else and use base R ifelse instead.
Changes in version 1.3.18-1.3.21 (2023-02-07)
Minor changes
- Small vignette updates and fixing typos / improved wording
Bug fixes
- due to a change from USCS that affected
GenomeInfoDb::getChromInfoFromUCSC("hg38") (see here for more
details), the minimum required version of GenomeInfoDb had to be
increased to 1.34.8. If you have troubles installing at least this
version, we recommend updating to the newest Bioconductor
version 3.16 or (without warranties) use the following line to
manually install the newest version directly from GitHub outside of
Bioconductor (not recommended):
BiocManager::install("Bioconductor/GenomeInfoDb)"
- small change in addData() so that peak IDs are stored with the same
name in the object in case the user-provided peak IDs have the
format chr:start:end as opposed to the required chr:start-end.
filterData() otherwise incorrectly discarded all peaks because of
the ID mismatch caused by the two different formats.
- fixed a rare edge case in filterGRNAndConnectGenes() that caused an
error when 0 TF-peak connections were found beforehand
Changes in version 1.3.17 (2023-01-26)
New features
- We are excited to announce that we added a new vignette for how to
use GRaNIE for single-cell data! We plan to update it regularly with
new information. Check it out here!
Changes in version 1.3.16 (2023-01-24)
New features
- significant updated to the package details vignette
- revisited and improved the internal logging and object history. The
time when a function was called is now added to the list name, which
allows the storage of multiple instances of the same function.
- new parameter in addData(): geneAnnotation_customHost to specify a
custom host and overriding the default and previously hard-coded
hostname when retrieving gene annotation data via biomaRt.
- the function getGRNConnections() can now also include the various
additional metadata for all type parameters and not only the default
type all.filtered.
Changes in version 1.3.15 (2023-01-20)
Bug fixes
- fixed an error that appeared in rare cases when a chromosome name
from either peak or RNA data could not be found in biomaRt such as
GL000194.1. Peaks from chromosomes with irretrievable lengths are
now automatically discarded.
- significant updates to the package details vignette
Changes in version 1.3.13-1.3.14 (2023-01-20)
New features
- the function plotDiagnosticPlots_peakGene() (which is also called
indirectly from addConnections_peak_gene() when setting
plotDiagnosticPlots = TRUE) now stores the plot data for the QC
plots from the first page into the GRN object. It is stored in
GRN@stats$peak_genes
- the columns of the result table from getGRNConnections() are now
explained in detail in the R help, and we reference this from the
Vignette and other places
- various significant Vignette updates
Bug fixes
- optimized the column names for the function getGRNConnections(),
which now does not return duplicate columns for particular cases
anymore
- improved printing in the log for the function filterData() and
addData()
- the loadExampleObject() function has been optimized and should now
force download an example object when requesting it.
- the package version as stored in the GRN object now works correctly.
Minor changes
- further code cleaning in light of the tidyselect changes in
version 1.2.0 to eliminate deprecated warnings
- the default gene types for addConnections_peak_gene() and
plotDiagnosticPlots_peakGene() have been homogenized and changed to
list(c("all"), c("protein_coding")). Before, the default was
list(c("protein_coding", "lincRNA")), but we decided to now split
this into two separate lists: Once for all genes irrespective of the
gene type and once for only protein-coding genes. As before, lincRNA
or other gene types can of course still be selected and chosen.
- various minor changes
Changes in version 1.3.12 (2022-12-22)
Bug fixes
- bug fix in plotCommunitiesEnrichment() that was introduced due to
the tidyselect 1.2.0 changes
Minor changes
- further code cleaning in light of the tidyselect changes in
version 1.2.0 to eliminate deprecated warnings
Changes in version 1.3.11 (2022-12-16)
Major changes
- the default URL for the example GRN object in loadExampleObject()
had to be changed due to changes in the IT infrastructure. The new
stable default URL is now
\url{https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds},
in the same Git repository that provides GRaNIE outside of
Bioconductor.
Bug fixes
- fixing bugs introduced due to the tidyverse 1.2.0 related code
cleaning
- other bugfix accidentally introduced in the previous commits
Changes in version 1.3.10 (2022-12-15)
Bug fixes
- revisited the import of TADs and made the code more error-prone and
fixed some bugs related to TADs. Importing TADs now works again as
before.
Minor changes
- code cleaning in light of the tidyselect changes in version 1.2.0 to
eliminate deprecated warnings
New features
- new argument for addConnections_peak_gene(): TADs_mergeOverlapping.
See the R help for more details.
Changes in version 1.3.9 (2022-12-14)
New features
- new argument for addConnections_peak_gene(): shuffleRNACounts. See
the R help for more details.
Minor changes
- first round of code cleaning in light of the tidyselect changes in
version 1.2.0 to eliminate deprecated warnings
Changes in version 1.3.4-1.3.8 (2022-12-06)
Major changes
- the topGO package is now required package and not optional anymore.
The reasoning for this is that the standard vignette should run
through with the default arguments, and GO annotation is the default
ontology so topGO is needed for this. Despite this package still
being optional from a strict workflow point of view, we feel this is
a better way and improves user friendliness by not having to install
another package in the middle of the workflow.
Minor changes
- in initializeGRN(), the objectMetadata argument is now checked
whether it contains only atomic elements, and an error is thrown if
this is not the case. As this list is not supposed to contain real
data, checking this prevents the print(GRN) function to
unnecessarily print the whole content of the provided object
metadata, thereby breaking the original purpose.
New features
- addTFBS() got two more arguments to make it more flexible. Now, it
is possible to specify the file name of the translation table to be
used via the argument translationTable, which makes it more flexible
than the previously hard-coded name "translationTable.csv. In
addition, the column separator for this file can now be specified
via the argument translationTable_sep
- Overlapping TFBS data with the peak is now more error-tolerant and
does not error out in case that some chromosome or contig names from
the TFBS BED files contain elements the size of which cannot be
retrieved online. This was the case for some contig names with the
suffix decoy, for example. If such elements are found, a warning is
now thrown and they are ignored as they are usually not wanted
anyway.
- in case a GRN objects contains 0 connections (e..g, because of too
strict filtering), subsequent functions as well as the print
function now give a more user-friendly warning / error message.
Changes in version 1.1.22-1.3.3 (2022-11-29)
New features
- additional normalization schemes have been implemented, including
GC-aware normalization schemes for peaks, and existing normalization
methods have been renamed for clarity. See ?addData for details.
- further reduced the package burden; the large genome annotation
packages are now more or less fully optional and only needed when a
GC-aware normalization has been chosen or when additional peak
annotation is wanted. However, in contrast to before, none of these
annotation packages are strictly required anywhere anymore. The
vignettes have been updated accordingly.
Minor changes
- various small changes in the code
- vignette updates
Changes in version 1.1.14-1.1.21 (2022-11-13)
Major changes and new features
- 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 and new features
- 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)
New features
- 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 and new features
- 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 and new features
- 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 and new features
- 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 and new features
- 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 and new features
- 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 and new features
- 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