Changes in version 1.5.3 o Changed `buildDataFromGraph()` so that it looks for organismal annotations in `keggInfo()`. o If `ncbi-geneid` was not available, `buildDataFromGraph()` would crash with 404. Now, it can use `ncbi-proteinid` if `ncbi-geneid` is missing. o Discovered by LY by building db for `"cvi"` o Small update on `sanitise()` Changes in version 1.4.2 o **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). Changes in version 1.4.1 o Fixed bug in vignette due to changes in `biomaRt` Changes in version 1.3.1 o Fixed main vignette title to match that of paper o Fixed `Unicode char' (U+301)` error (had a tilde as `\'\i` in bibfile) o Added citation to BMC article Changes in version 1.1.6 o Fixed vignette indices Changes in version 1.1.5 o Added full vignette on the zebrafish dataset o Small modifications to the Mus musculus vignette Changes in version 1.1.4 o Added a full vignette showing a case study on Mus musculus o Functions `getCom` and `getGraph` are exported now o Added `DT` and other packages to `suggests` o Small fixes for `BiocCheck` Changes in version 1.1.3 o Version 1.1.2 did not skip such test Changes in version 1.1.2 o Disabled `buildGraphFromKEGGREST` test in 32-bit Windows due to its memory usage Changes in version 0.99.6 o Small corrections in vignette o Removed `rm` calls Changes in version 0.99.5 o Small correction in vignette o Version bump to see if bioc build is bugged Changes in version 0.99.4 o Moved contents of `NEWS.md` to NEWS o Deleted most of `data-raw` folder, moved the rest to `inst/script` o Removed redundant `Authors` field in DESCRIPTION o Removed `class(data) != "FELLA.DATA"` by using built-in `is.FELLA.DATA` Changes in version 0.99.3 o Version bump (biomaRt down?) Changes in version 0.99.2 o Fixed more doc links Changes in version 0.99.1 o Fixed doc links (hopefully) o Updated funding in vignette o Travis will only test the devel branch Changes in version 0.99.0 o Submission to Bioconductor Changes in version 0.5.14 o Small bugs Changes in version 0.5.13 o Small bug fixes Changes in version 0.5.12 o Small bug fixes Changes in version 0.5.11 o Fixed calls to `sapply` and `1:n` Changes in version 0.5.10 o Adding GO CC is now in `dontrun`, takes too long (12s) Changes in version 0.5.9 o Fixed vignette: converted pdf images to eps and added them Changes in version 0.5.8 o Removed `broser()` calls o Removed some commented code o Expanded doc on `launchApp` o Removed the old gone report functionality in the app (might bring it back eventually) o Added captures of the graphical interface to the main vignette Changes in version 0.5.7 o Slight changes in vignette (affiliations) o Fixed `generateEnzymesTable`: now it can also add the GO terms inside each enzyme o Modified `addGOToGraph`: now it will add only the GO labels, without similarity score, provided that `GOterm = NULL` o Improved doc in result exports: `generateResultsTable`, `generateEnzymesTable`, `generateResultsGraph`, `addGOToGraph` and `plotGraph`. - Merged all the doc - Added references - Expanded details Changes in version 0.5.6 o 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 o References are now in template files Changes in version 0.5.5 o Improved doc in `FELLA.DATA` object creation - Fused 3 functions - Added references - Expanded details Changes in version 0.5.4 o Added progress bars to shiny app for: - Loading database - Enriching - Adding GO similarity o Added simple legend for GO similarity Changes in version 0.5.3 o Added `CITATION` file o Added some cites to doc Changes in version 0.5.2 o 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 Changes in version 0.5.1 o Small modifications on Travis and `is-.R` Changes in version 0.5.0 o Fixed bibliography in vignette o Fixed missing table in vignette o Changed mechanisms when handling existing directories. Now the writing is stopped instead of overwriting and the automatic names are more meaningful. o New naming convention for databases. Meaningful names with creation date, organism and KEGG version. o Updated unit testing and argument checking accordingly Changes in version 0.4.13 o Temporarily downgraded R dependency to version 4.3 o Bug on the `biomaRt` query was actually due to their package being outdated. Updating fixed it. o Small changes in functions (exports) to pass `check()` o Small fixes on Shiny App o Added vignette Changes in version 0.4.12 o Travis modification Changes in version 0.4.11 o Small changes on functions and DESCRIPTION Changes in version 0.4.10 o Trying Travis Changes in version 0.4.9 o Small changes in plotting functions Changes in version 0.4.8 o Fixed the `FELLA.sample` file so that it contains the metadata o Added the `getInfo` function for getting the metabata, with corresponding unit testing o Fixed minor writing mistakes o `loadMatrix` can no longer be `"all"` o `AllArguments.R` now has `loadMatrix`, `databaseDir`, `internalDir` o 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 Changes in version 0.4.7 o Improved vignette text and added Bioconductor style o Added `BiocStyle` as a dependency To do: o General check of arguments and documentation o Quantitative input? o Elaborate on this vignette or build another one for publication Changes in version 0.4.6 o Removed the infamous `splitByCC` part (from `checkArguments`, the conditional on the `plot` method and from the vignette) o 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. Changes in version 0.4.5 o Modified size p-value computation. Now it is more efficient and consistent Changes in version 0.4.4 o Fused `checkArguments` into `AllArguments.R` o Deleted the generic `summary` as it is not necessary. Now the same can be achieved using `show` only, and this avoids method dispatch issues. Changes in version 0.4.3 o Added the `summary` method for `FELLA.DATA` objects o Fixed some dependencies in methods o Separated `mytriangle` in function `plotGraph` o Renamed functions (`is-.R`, `plotLegend.R`) o Updated sample data documentation Changes in version 0.4.2 o Added doc template for the statistical normalisation o Removed p-values from table o Improved `generateResultsTable` function o Improved `runDiffusion` and `runPagerank` at the code level and avoided checking arguments Changes in version 0.4.1 o Added accessor to `status` and substituted all the calls o Addition of GO terms works Changes in version 0.4.0 o Removed some superfluous arguments: askplots, filename, BIMODAL o Aggregated `get-.R` and `list-.R` functions in single files o Cleaned part of: `AllMethods`, `exportResults`, `generate-` o Fixed unit testing o Fixed runnable examples o Fixed vignette o Rebuilt example data o Improved argument handling. `method` can no longer be `"all"` and handles a unique method now, but `methods` can pass a vector of methods instead o Passes `check()` and `BiocCheck(".")` Changes in version 0.3.3 o Improved argument documentation (still work to do) o Fused individual dummy functions that contained the commented parameters o Added `list-()` functions o Removed `p.adjust` from diffusion and pagerank o Improved unit testing To do: o Fix documentation of changed functions o Try to better isolate functions (e.g. `plot` and `generateResultsGraph` do too many things at once...) o Quantitative input? o Delete repetitive code o Use `checkArguments` in main functions o Improve `AllMethods`: use accessors, clean code... Changes in version 0.3.2 o Switched from `pValues` to `pScores` (except in `hypergeom`) Changes in version 0.3.1 o Removed `rcytoscapejs` dependency Changes in version 0.3.0 o Fixed vignette o 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 o Shiny app: - Removed tabs, has only 4 now - Left only interactive plot - Table is now from `DT` To do: o Fix documentation of changed functions o Try to better isolate functions (e.g. `plot` and `generateResultsGraph` do too many things at once...) o Quantitative input? o Improve function documentation (use templates) to supress warnings o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN) o What to do about the p-values? Changes in version 0.2.6 o Fixed indentation o Fixed long lines o Added NEWS file o Fixed examples To do: o Vignette breaks, top priority o Quantitative input? o Improve function documentation (use templates) to supress warnings o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN) o What to do about the p-values? Changes in version 0.2.5 Some minor changes to accomodate Bioconductor's standards o Update `R` version o Add `R` file to the `testthat` folder o Add GO biocView To do from Bioconductor o Vignette breaks o Add NEWS file o Fix indentation o Fix long lines (<80) o Add runnable examples: - buildDataFromGraph - buildGraphFromKEGGREST - loadKEGGdata To do o Quantitative input? o Improve function documentation (use templates) to supress warnings o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN) Changes in version 0.2.4 o 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... Changes in version 0.2.3 o Fixed CREB website link o Added the option to specify the damping factor in pagerank o Changed default damping factor to 0.85 Changes in version 0.2.2 o Fixed table export (`stringsAsFactors` was not disabled when creating the data.frame). o 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/). o The shiny app exports tables with the full enzyme data and simply as a text gene list as well. Changes in version 0.2.1 The shiny app has been updated. o 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`. o The colors and shapes have been updated as well, to be consistent with our notation. To do o The labels of the nodes are not sorted by length. Short labels can be really weird... Changes in version 0.2.0 Added the shiny app as a developer option. It requires the following packages o shiny o DT o xtable o knitr o rcytoscapejs Changes in version 0.0.999 o 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 o Further versions should include interactive plots and applications for an easier usage