- MIRit
- Graph
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65dbe7b
(HEAD -> devel, origin/devel, origin/HEAD)
Fixed a bug that prevented the correct use of correlation analysis. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2025-03-19 10:40:54 +0000;
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179a4dd
Fixed a bug that prevented the use of local miRTarBase copies. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2025-03-19 10:15:31 +0000;
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2294ad9
Fix in the GitHub README along with a version bump. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2025-03-14 13:18:29 +0000;
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0756743
The getTargets() function now supports the use of a local copy of miRTarBase. Package version has been fixed. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2025-03-14 13:06:32 +0000;
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2e56493
The getTargets() function now allows to use a local version of miRTarBase through the local parameter. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2025-03-14 12:57:21 +0000;
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57bfd48
bump x.y.z version to odd y following creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>
2024-10-29 11:27:09 -0400;
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d4af30f
(origin/RELEASE_3_20, RELEASE_3_20)
bump x.y.z version to even y prior to creation of RELEASE_3_20 branch by
J Wokaty <jennifer.wokaty@sph.cuny.edu>
2024-10-29 11:27:09 -0400;
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e42dfe9
The README file has been updated and the version has been bumped. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-10-23 14:26:17 +0000;
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6706b7f
This commits consists of a simple version bump to drive BBS. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-10-23 14:21:52 +0000;
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b606ccf
This new version corrects the version bump and adds what's changed in the NEWS file. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-10-23 14:09:07 +0000;
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106d031
The issues that prevented the completion of R CMD check has been fixed. Moreover, MIRit now uses miRTarBase version 10. Also, the vignette has been reduced. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-10-23 13:59:02 +0000;
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3abb821
bump x.y.z version to odd y following creation of RELEASE_3_19 branch by
J Wokaty <jwokaty@users.noreply.github.com>
2024-04-30 11:53:58 -0400;
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ed1b3ba
(origin/RELEASE_3_19, RELEASE_3_19)
bump x.y.z version to even y prior to creation of RELEASE_3_19 branch by
J Wokaty <jwokaty@users.noreply.github.com>
2024-04-30 11:53:58 -0400;
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3a2a2cd
Version 0.99.13: a minor fix was made to fix the undefined variables note during R CMD check. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-02-12 14:24:04 +0000;
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e26173d
Version 0.99.12: this version includes several improvements, including a completely revised vignette where all chunks are evaluated, minor tweaks to default values for differential expression analysis, and some bug fixes to the error bars in the `plotDE()` function. Other issues, such as artifacts in show methods, lacks in documentation, and dependence in DESCRIPTION, have been addressed too. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-02-12 13:37:25 +0000;
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c3a4677
Version 0.99.11: this new version introduces the possibility of limiting validated targets retrieval from miRTarBase to only those interactions supported by extensive experimental evidence. Moreover, minor fixes were made to the vignette, documentation, and internal data. Finally, some examples have been redefined to reduce checking time. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-02-07 09:37:16 +0000;
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058ea56
Version 0.99.10: this patch introduces a minor fix for one unit test. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-02-01 13:12:28 +0000;
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353dc83
Version 0.99.9: with this version, significant p-values originating from functional enrichment analyses now include extreme values. Further, examples have been shortened and unit tests now use smaller datasets. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-02-01 12:11:55 +0000;
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770c4cb
Version 0.99.8: this patch further reduces R CMD check time by limiting unnecessary examples and by using smaller datasets for unit tests. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-01-31 16:02:41 +0000;
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af6a9bf
Version 0.99.7: this version introduces parallel computing capabilities for the 'mirnaIntegration()' function. This is particularly useful for Boschloo's exact test, whose execution is now faster. Moreover, the test suite has been redefined to reduce running times. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-01-31 12:25:33 +0000;
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b8d29fd
Version 0.99.6: The testing suite has been redefined to allow different results for different versions of packages employed in differential expression analysis. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-01-30 13:59:40 +0000;
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7372b32
Version 0.99.5: this version fixes a bug in a bug in the `batchCorrection()` function that prevented the correct use of this function with newer versions of the `MultiAssayExperiment` package. by
jacopo-ronchi <jacopo.ronchi@unimib.it>
2024-01-30 11:38:23 +0000;
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09dd844
Version bump to 0.99.4 to drive a new build on Bioconductor SPB. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-29 15:28:51 +0100;
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af61de5
Version 0.99.3 fixes a bug that prevented the correct use of a functional progress bar in the 'topologicalAnalysis()' function. Moreover, the example in 'addDifferentialExpression()' function has been updated to reduce running time. Finally, the code has been re-styled using the latest biocthis template. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-15 16:54:07 +0100;
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1b94c1b
In version 0.99.2 the possibility of filtering miRNA augmented pathways based on a minimum and maximum number of nodes has been added and documented. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-15 11:22:00 +0100;
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f5b58dd
Version bump from 0.99.0 to 0.99.1. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-13 12:48:56 +0100;
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c38fbf0
The code has been restyled with the styleR package to adhere to Bioconductor guidelines. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-13 10:37:20 +0100;
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ceabf42
The testing suite has been improved to reduce running time during R CDM check. Moreover, pathways and gene-sets retrieved during functional enrichment analyses and TAIPA are now saved to cache to reduce running times when checking examples and vignette building. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-13 10:25:05 +0100;
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3d48b7c
The test for ORA enrichment has been updated because the results changed. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-11 11:41:57 +0100;
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2636aa6
The README has been updated to allow GitHub installation during Bioconductor submission. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-11 10:51:29 +0100;
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e4c850e
The license link was fixed to point to the GPL-3 license. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-06 11:47:54 +0100;
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c1ed086
The badges in README has been updated to only contain valid links. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-06 11:44:57 +0100;
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5b3a365
The 'dev' folder has been removed prior to Bioconductor submission. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-06 11:12:15 +0100;
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b3cf8f1
The indentation and formatting of R code has been fixed with styleR. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-05 17:18:07 +0100;
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e157956
Small fixes were made to further limit warnings during BiocCheck(). Now the test passes with 0 warnings and 0 errors. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-05 17:06:34 +0100;
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9c038ef
This commit fixes numerous warnings and notes arising during Bioccheck(). Specifically, the majority of corrected notes is related to code formatting. Further, notes regarding missing documentation "\value" section were addressed. Also, dontrun examples have been converted to donttest. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-05 13:22:20 +0100;
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8cced21
The space under the logo in the home page has been slightly reduced. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-04 12:11:03 +0100;
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eded126
The responsiveness of the documentation site has benn adjusted for mobile devices. Furthermore, the home page style is now fixed once for all. The README has also been updated to include an 'overview' title. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-04 11:56:50 +0100;
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cffc71f
The css style is now correctly applied only to the home page. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-04 11:24:52 +0100;
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526fe4c
Updated extra.css to apply the changes only to the home page. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-04 10:38:26 +0100;
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f5dd9ad
Added a file called extra.css to slightly customize the appearence of the home page. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-12-04 10:04:37 +0100;
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7b22b38
Trying the litera theme for the documentation website. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-01 17:32:45 +0100;
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50a28fe
Trying the flatly bootstrap template. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-01 12:44:43 +0100;
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946fdd5
Removing the pkgdown workflow. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-01 12:20:44 +0100;
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0237ffd
A GitHub workflow for manually creating the documentation website has been created. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-12-01 11:58:18 +0100;
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01cd6e1
Small fixes have been made to correctly produce the documentation website. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-30 15:54:51 +0100;
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6dcce75
The SVG logo has been fixed for markdown rendering and is now used in README, vignettes and pkgdown. Favicons have been re-generated again. Furthermore, the documentation website has been designed newly based on bootstrap 5. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-30 15:20:48 +0100;
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d80d13e
The authors have been updated to include the funder. Moreover, some initial tweaks have been apported to the pkgdown website and README. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-30 11:05:53 +0100;
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2668b80
The GitHub workflow has been updated to included scheduled runs. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-29 17:24:32 +0100;
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bbfdfc4
The MIRit logo has been re-designed. The README and vignette files have been updated accordingly. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-29 17:23:50 +0100;
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288811e
The README was updated to change citation style. Moreover, the use of sapply() and 1:n in two occurrences was changed to vapply() and seq(), respectively. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 16:42:27 +0100;
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c57ba00
The tests involved in checking the responsivness of external resources are now skipped on GitHub actions and Bioconductor. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 14:37:07 +0100;
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3a90fa2
Added a skip on windows when testing the responsiveness of ensembl. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 14:10:21 +0100;
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b797d35
Added a skip on windows condition when testing the responsiveness of miRTarBase. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 13:36:36 +0100;
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11dea0e
README citation section has been fixe to show english output. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 12:26:31 +0100;
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20c0ebd
The tests for the creation of miRNA augmented pathways, along with the tests for target retrieval have been updated to fix some errors during R-CMD check. Furthermore, the R-CMD badge on the README has been fixed. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-28 11:17:35 +0100;
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2820ce7
The test suite has been updated to avoid the use of snapshot testing. Now almost all the tests only rely on simple expectations. Furthermore, small fixes were made to the README and to the mirnaIntegration() function. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-27 17:04:21 +0100;
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b52aa7a
The MIRit preprint is now specified in the CITATION file. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-27 10:52:20 +0100;
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439e986
Update check-bioc.yml to include workflow dispatch, so that it can be run on directly on GitHub. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-24 19:10:54 +0100;
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160e821
The styler package was used to re-format the code to match the Bioconductor coding guidelines. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-24 17:00:08 +0100;
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a7dc82d
Fixed a bug with cross-links in documentation website. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-24 16:38:46 +0100;
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fbccc02
This commit updates the README file and moves the logo to man/figures so that it can be used from the vignette, README and the documentation website. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-24 16:09:35 +0100;
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0c279dd
GitHub Actions have been updated to include unit testing, test coverage and documentation website generation via pkgdown. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-24 11:24:19 +0100;
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8a07d1b
The man page for the whole package has been updated. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:40:18 +0100;
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47d2507
This commit adds the configuration for the GitHub workflow that is needed for testing the package on Linux, Windows and macOS, and much more. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:24:28 +0100;
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57616ea
R project file is no more tracked with git, as required by Bioconductor. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:17:35 +0100;
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6b90d69
Merge branch 'main' of github.com:jacopo-ronchi/MIRit into main by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:13:20 +0100;
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448441c
Biocthis was used to configure Bioconductor-friendly templates for the DESCRIPTION, README, NEWS, and citation. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:09:21 +0100;
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4e8438b
Delete .Rbuildignore by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:03:59 +0100;
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d09db7a
Delete MIRit.Rproj by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 16:03:46 +0100;
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b91bdb6
The test suite received an update to allow specific warnings, along with an updated snapshot of miRNA augmented networks. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-23 13:56:20 +0100;
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89aa09f
This commit moves different dependences to Suggests, and adds the possibility to use them conditionally. This removes the note during RMD check. Furthermore, the vignette has been updated to remove some unnecessary text. Internal data has also been compressed more efficiently and package size reduced. Also, some dependences have been removed. Finally, some tests have been revised and updated. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-22 17:26:07 +0100;
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8b456a4
This commit includes some fixes in the documentation along with a new option to include or not include a progress bar during TAIPA. Further, other fixes in the DESCRIPTION and NAMESPACE were made to prevent errors during RMD check. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-22 14:24:56 +0100;
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9d73919
This commit introduces a novel function, called 'batchCorrection()', that allows to remove batch effects from expression matrices before conducting correlation analysis. The vignette and the help pages have been updated accordingly. Moreover, other fixes were made to fix some of the warnings and notes occurring during RMD check. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-15 17:02:30 +0100;
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d08afeb
This is a major release. MIRit package is preparing for the Bioconductor submission and the code is being reviewed to adhere to the Bioconductor guidelines. In this review: - a new suite of unit tests have been included to monitor the behaviour of MIRit in future releases and to make sure that everything keeps working appropriately; - different fixes were apported to pass RMD check without errors and warnings (even if examples and tests will require additional tweaks); - the documentation files have been updated and cross-references were fixed in order to have a fully comprehensive manual; - the DESCRIPTION and NAMESPACE files have been updated to correctly load and use MIRit. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-09 16:43:22 +0100;
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1b2a9a3
Fixed a bug in the edgeR differential expression pipeline that prevented the use of pAdjustment equal to 'none'. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-11-07 12:27:10 +0100;
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17e0200
In this commit the vignette has been updated and it is now concluded. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-30 12:03:35 +0100;
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aba31c8
Small refinements were apported to the vignette to include better plots. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-10-29 14:16:28 +0100;
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e35e0b7
This commit introduces a fix for a bug in the plotDE() function that caused wrong y position for significance labels. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-10-29 14:14:57 +0100;
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d6bce68
In this version the vignette was updated along with its references and missing sections has been added. Images have also been included and refined along with captions, cross-references and tables. Moreover, internal data now stores an example of TAIPA for the thyroid cancer dataset, and this object can now be accessed from the loadExamples() function. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-27 13:48:34 +0200;
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7836fd4
The MIRit vignette has been updated. However, some sections are missing and some other sections must be fixed. by
Jacopo Ronchi <j.ronchi2@campus.unimib.it>
2023-10-26 17:07:32 +0200;
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c58b897
The documentation of several visualization function has been updated to support hexadecimal colors. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-13 11:16:14 +0200;
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a07a82c
Now the visualization functions in MIRit support the specification of colors as hexadecimal codes. Further, two samll fixes in mirVariantPlot() and visualizeNetwork() has been added. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-13 11:14:25 +0200;
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b792de4
Fixed a small bug that prevented the creation of trackplots withou the title. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-12 16:58:00 +0200;
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14ffce0
This commit adds the possibility of plotting only specific features in the visualizeNetwork() function, so that, for messy graphs, the user can maintain only specific nodes. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-10 10:49:25 +0200;
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3cefb68
This commit introduces a show method for the IntegrativePathwayAnalysis class. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-09 17:07:47 +0200;
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4947cc4
The TAIPA pipeline is now divided in two distinct functions. The first one is 'preparePathways()', which creates miRNA-augmented pathways from the defined database, while 'topologicalAnalysis()' only computes p-values and calculates their statistical significance. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-09 16:55:33 +0200;
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073eaa0
This version changes the formula used to determine p-values in TAIPA to prevent them from being equal to zero. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-09 10:03:33 +0200;
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ef56b80
This commit fixes different bugs in the association of disease-SNPs occurring in DE-miRNA loci, adds the support for variants occurring in miRNA host genes, and updates the mirVariantPlot function for creating useful track plots to visually represent these associations. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-06 15:21:30 +0200;
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b07b9d1
The code for pathway score calculation, and the code for determining score significance via permutations has been optimized. After this release TAIPA results 2/3 times faster than before. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-03 16:11:07 +0200;
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30b7aee
Solved a git conflict in the previous commits. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-03 14:43:32 +0200;
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adc7b3f
Solved a typo introduce in the last commit and added a fix that prevented startup messages from org databases. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-03 14:18:28 +0200;
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514bcbd
Node conversion from ENTREZID to SYMBOL has been re-implemented to allow parallelized access to organism annotation database. As a result, node conversion is now much faster. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-03 13:48:26 +0200;
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84b7fa9
Node conversion from ENTREZID to SYMBOL has been re-implemented to allow parallelized access to organism annotation database. As a result, node conversion is now much faster. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-10-03 13:48:26 +0200;
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321e70d
Minor fix in the unified ggplot2 theme that restores grid lines as theme_bw(). by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-28 15:34:06 +0200;
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282e8a4
Minor fix in plotDE() that allows to control legend position with nameAsTitle set to TRUE. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-28 15:02:57 +0200;
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a1bdf22
Minor fix that corrected significance label position in plotDE(). by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-28 14:45:12 +0200;
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0d90fc7
PlotDE() function has been edited to group expression levels on the x-axis based on gene. Instead, the color scale now refers to biological conditions. Furthermore, a new option has been added to show the gene name as title. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-28 12:54:46 +0200;
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fedaa7b
Several plotting functions has been updated to include multiple plotting parameters, namely legend position, number of borders, line width of borders, grid lines, font size and font family. All these parameters are managed by an helper function that applies a custom ggplot2 theme that is consistent for all plotting functions provided by MIRit. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-27 17:11:58 +0200;
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37c24ad
This version fixes a serious bug that caused the inclusion of non-significant miRNA-target pairs during pathway score calculation in TAIPA. by
Jacopo Ronchi <jacopo.ronchi@unimib.it>
2023-09-25 14:59:49 +0200;