NEWS

---

FELLA 1.5.3

• Changed 'buildDataFromGraph()' so that it looks for organismal annotations in 'keggInfo()'.
• If 'ncbi-geneid' was not available, 'buildDataFromGraph()' would crash with 404. Now, it can use 'ncbi-proteinid' if 'ncbi-geneid' is missing.
• Discovered by LY by building db for '"cvi"'
• Small update on 'sanitise()'

FELLA 1.4.2

• **The REST KEGG service changed and modules are no longer listable by organism**. 'FELLA' now chooses modules that have at least one organismal gene. This seems equivalent to picking the modules from 'keggLink("genome", "module")', but the latter is slow (90s).

FELLA 1.4.1

• Fixed bug in vignette due to changes in 'biomaRt'

FELLA 1.3.1

• Fixed main vignette title to match that of paper
• Fixed ‘Unicode char’ (U+301)‘ error (had a tilde as '\’\i' in bibfile)
• Added citation to BMC article

FELLA 1.1.6

• Fixed vignette indices

FELLA 1.1.5

• Added full vignette on the zebrafish dataset
• Small modifications to the Mus musculus vignette

FELLA 1.1.4

• Added a full vignette showing a case study on Mus musculus
• Functions 'getCom' and 'getGraph' are exported now
• Added 'DT' and other packages to 'suggests'
• Small fixes for 'BiocCheck'

FELLA 1.1.3

• Version 1.1.2 did not skip such test

FELLA 1.1.2

• Disabled 'buildGraphFromKEGGREST' test in 32-bit Windows due to its memory usage

FELLA 0.99.6

• Small corrections in vignette
• Removed 'rm' calls

FELLA 0.99.5

• Small correction in vignette
• Version bump to see if bioc build is bugged

FELLA 0.99.4

• Moved contents of 'NEWS.md' to NEWS
• Deleted most of 'data-raw' folder, moved the rest to 'inst/script'
• Removed redundant 'Authors' field in DESCRIPTION
• Removed 'class(data) != "FELLA.DATA"' by using built-in 'is.FELLA.DATA'

FELLA 0.99.3

• Version bump (biomaRt down?)

FELLA 0.99.2

• Fixed more doc links

FELLA 0.99.1

• Fixed doc links (hopefully)
• Updated funding in vignette
• Travis will only test the devel branch

FELLA 0.99.0

• Submission to Bioconductor

FELLA 0.5.14

• Small bugs

FELLA 0.5.13

• Small bug fixes

FELLA 0.5.12

• Small bug fixes

FELLA 0.5.11

• Fixed calls to 'sapply' and '1:n'

FELLA 0.5.10

• Adding GO CC is now in 'dontrun', takes too long (12s)

FELLA 0.5.9

• Fixed vignette: converted pdf images to eps and added them

FELLA 0.5.8

• Removed 'broser()' calls
• Removed some commented code
• Expanded doc on 'launchApp'
• Removed the old gone report functionality in the app (might bring it back eventually)
• Added captures of the graphical interface to the main vignette

FELLA 0.5.7

• Slight changes in vignette (affiliations)
• Fixed 'generateEnzymesTable': now it can also add the GO terms inside each enzyme
• Modified 'addGOToGraph': now it will add only the GO labels, without similarity score, provided that 'GOterm = NULL'
• Improved doc in result exports: 'generateResultsTable', 'generateEnzymesTable', 'generateResultsGraph', 'addGOToGraph' and 'plotGraph'. - Merged all the doc - Added references - Expanded details

FELLA 0.5.6

• Improved doc in enrichment techniques: - Merged 5 functions: 'defineCompounds', 'runHypergeom', 'runDiffusion', 'runPagerank', 'enrich' - Expanded details: formulation, how to compute scores, null model - Added references - Centralised examples
• References are now in template files

FELLA 0.5.5

• Improved doc in 'FELLA.DATA' object creation - Fused 3 functions - Added references - Expanded details

FELLA 0.5.4

• Added progress bars to shiny app for: - Loading database - Enriching - Adding GO similarity
• Added simple legend for GO similarity

FELLA 0.5.3

• Added 'CITATION' file
• Added some cites to doc

FELLA 0.5.2

• Shiny app - Fixed bug: table not showing up - Documentation has been improved - Fixed bug: empty network led to error - Now exporting a network takes into account 'thresholdConnectedComponent' as well (it did not until now) - Modified logo size and title

FELLA 0.5.1

• Small modifications on Travis and 'is-.R'

FELLA 0.5.0

• Fixed bibliography in vignette
• Fixed missing table in vignette
• Changed mechanisms when handling existing directories. Now the writing is stopped instead of overwriting and the automatic names are more meaningful.
• New naming convention for databases. Meaningful names with creation date, organism and KEGG version.
• Updated unit testing and argument checking accordingly

FELLA 0.4.13

• Temporarily downgraded R dependency to version 4.3
• Bug on the 'biomaRt' query was actually due to their package being outdated. Updating fixed it.
• Small changes in functions (exports) to pass 'check()'
• Small fixes on Shiny App
• Added vignette

FELLA 0.4.12

• Travis modification

FELLA 0.4.11

• Small changes on functions and DESCRIPTION

FELLA 0.4.10

• Trying Travis

FELLA 0.4.9

• Small changes in plotting functions

FELLA 0.4.8

• Fixed the 'FELLA.sample' file so that it contains the metadata
• Added the 'getInfo' function for getting the metabata, with corresponding unit testing
• Fixed minor writing mistakes
• 'loadMatrix' can no longer be '"all"'
• 'AllArguments.R' now has 'loadMatrix', 'databaseDir', 'internalDir'
• Shiny app: - Fixed the database error when no database is present - Fixed table error when the graph was empty (e.g. hypergeom) - Adding a GO term is now functional again. Added several biomaRt/GO options. - GO term changes plot legend - Changes in the UI (text, new widgets for GO term) - GO example autofills all the new widgets

FELLA 0.4.7

• Improved vignette text and added Bioconductor style
• Added 'BiocStyle' as a dependency To do:
• General check of arguments and documentation
• Quantitative input?
• Elaborate on this vignette or build another one for publication

FELLA 0.4.6

• Removed the infamous 'splitByCC' part (from 'checkArguments', the conditional on the 'plot' method and from the vignette)
• Now the option is to filter out small CCs but still work with a single graph ('thresholdConnectedComponent' still exists). Therefore, function 'generateResultsGraph' can only return a graph, being more intuitive.

FELLA 0.4.5

• Modified size p-value computation. Now it is more efficient and consistent

FELLA 0.4.4

• Fused 'checkArguments' into 'AllArguments.R'
• Deleted the generic 'summary' as it is not necessary. Now the same can be achieved using 'show' only, and this avoids method dispatch issues.

FELLA 0.4.3

• Added the 'summary' method for 'FELLA.DATA' objects
• Fixed some dependencies in methods
• Separated 'mytriangle' in function 'plotGraph'
• Renamed functions ('is-.R', 'plotLegend.R')
• Updated sample data documentation

FELLA 0.4.2

• Added doc template for the statistical normalisation
• Removed p-values from table
• Improved 'generateResultsTable' function
• Improved 'runDiffusion' and 'runPagerank' at the code level and avoided checking arguments

FELLA 0.4.1

• Added accessor to 'status' and substituted all the calls
• Addition of GO terms works

FELLA 0.4.0

• Removed some superfluous arguments: askplots, filename, BIMODAL
• Aggregated 'get-.R' and 'list-.R' functions in single files
• Cleaned part of: 'AllMethods', 'exportResults', 'generate-'
• Fixed unit testing
• Fixed runnable examples
• Fixed vignette
• Rebuilt example data
• Improved argument handling. 'method' can no longer be '"all"' and handles a unique method now, but 'methods' can pass a vector of methods instead
• Passes 'check()' and 'BiocCheck(".")'

FELLA 0.3.3

• Improved argument documentation (still work to do)
• Fused individual dummy functions that contained the commented parameters
• Added 'list-()' functions
• Removed 'p.adjust' from diffusion and pagerank
• Improved unit testing To do:
• Fix documentation of changed functions
• Try to better isolate functions (e.g. 'plot' and 'generateResultsGraph' do too many things at once...)
• Quantitative input?
• Delete repetitive code
• Use 'checkArguments' in main functions
• Improve 'AllMethods': use accessors, clean code...

FELLA 0.3.2

• Switched from 'pValues' to 'pScores' (except in 'hypergeom')

FELLA 0.3.1

• Removed 'rcytoscapejs' dependency

FELLA 0.3.0

• Fixed vignette
• Modifications to several functions, addressing: - Proper handling of GO labels - now can be used in many species - 'addCellularComponentToGraph' is now 'addGOToGraph' - New dependency: biomaRt - Plotting functions have been simplified, but still need work - Graph building has been improved
• Shiny app: - Removed tabs, has only 4 now - Left only interactive plot - Table is now from 'DT' To do:
• Fix documentation of changed functions
• Try to better isolate functions (e.g. 'plot' and 'generateResultsGraph' do too many things at once...)
• Quantitative input?
• Improve function documentation (use templates) to supress warnings
• Change 'rcytoscapejs' dependency to 'visNetwork' (in CRAN)
• What to do about the p-values?

FELLA 0.2.6

• Fixed indentation
• Fixed long lines
• Added NEWS file
• Fixed examples To do:
• Vignette breaks, top priority
• Quantitative input?
• Improve function documentation (use templates) to supress warnings
• Change 'rcytoscapejs' dependency to 'visNetwork' (in CRAN)
• What to do about the p-values?

FELLA 0.2.5

Some minor changes to accomodate Bioconductor's standards

• Update 'R' version
• Add 'R' file to the 'testthat' folder
• Add GO biocView

To do from Bioconductor

• Vignette breaks
• Add NEWS file
• Fix indentation
• Fix long lines (<80)
• Add runnable examples: - buildDataFromGraph - buildGraphFromKEGGREST - loadKEGGdata

To do

• Quantitative input?
• Improve function documentation (use templates) to supress warnings
• Change 'rcytoscapejs' dependency to 'visNetwork' (in CRAN)

FELLA 0.2.4

• Minor tweaks in the plotting function. Has more flexibility and can use ‘tkplot' as well (for image generation purposes), or force layout. This function should be really improved, it’s not that hard...

FELLA 0.2.3

• Fixed CREB website link
• Added the option to specify the damping factor in pagerank
• Changed default damping factor to 0.85

FELLA 0.2.2

• Fixed table export ('stringsAsFactors' was not disabled when creating the data.frame).
• Added the function 'generateEnzymesTable' to build a table with the EC numbers, along with the genes (entrez) within them and the associated GO labels (http://www.geneontology.org/).
• The shiny app exports tables with the full enzyme data and simply as a text gene list as well.

FELLA 0.2.1

The shiny app has been updated.

• Now the rcytoscape part has clickable links. This is due to a change in the r-cytoscape.js (https://github.com/cytoscape/r-cytoscape.js/) package that changes the 'href' node attribute to 'tooltip'.
• The colors and shapes have been updated as well, to be consistent with our notation.

To do

• The labels of the nodes are not sorted by length. Short labels can be really weird...

FELLA 0.2.0

Added the shiny app as a developer option. It requires the following packages

• shiny
• DT
• xtable
• knitr
• rcytoscapejs

FELLA 0.0.999

• This is the first version of this package. It contains: o Basic enrichment functions: hypergeom, diffusion, pagerank o Null models: normal or Monte Carlo o Export options: to tables or graphs o Plotting capabilities o Possibility of custom background
• Further versions should include interactive plots and applications for an easier usage