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 1.4.2/1.5.2
------------------------
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 1.4.1/1.5.1
------------------------
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
------------------------
+ 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