GRaNIE merge requestshttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests2023-12-10T13:23:57Zhttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/16Master2023-12-10T13:23:57ZMaksim KholmatovMasterSmall changes fixing broken link to the logo.
Plus remove this annoying black box left of the Vignettes link.
![image](/uploads/a015ce1a94aa1ba9e57b8dcc4440f152/image.png)
`pkgdown` still needs to be re-ran to generate the correct web p...Small changes fixing broken link to the logo.
Plus remove this annoying black box left of the Vignettes link.
![image](/uploads/a015ce1a94aa1ba9e57b8dcc4440f152/image.png)
`pkgdown` still needs to be re-ran to generate the correct web page. But for me it fails due to GRaNIE_singleCell_eGRNs vignette missing:
<details>
<summary>pkgdown error</summary>
```
-- Building articles -----------------------------------------------------------
Error:
! in callr subprocess.
Caused by error in `data_articles_index(pkg)`:
! Vignettes missing from index: GRaNIE_singleCell_eGRNs, quickStart
ℹ See `$stdout` and `$stderr` for standard output and error.
```
</details>Christian ArnoldChristian Arnoldhttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/15grn heatmap comparison2023-07-03T11:46:26ZRim Moussagrn heatmap comparisonincluded a function to compare regions / tf activity across GRNsincluded a function to compare regions / tf activity across GRNsGRaNIEversehttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/14Revert "Merge branch 'TFBS-update' into 'master'"2023-02-27T15:28:53ZChristian ArnoldRevert "Merge branch 'TFBS-update' into 'master'"This reverts merge request !13This reverts merge request !13https://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/13TFBS update2023-02-27T15:28:06ZRim MoussaTFBS updateUpdate on how to import TFBS into the pipeline:
in addition to the previous custom import, the GRaNIE pipeline can now internally use the JASPAR database to import motifs and overlap them with peaks.Update on how to import TFBS into the pipeline:
in addition to the previous custom import, the GRaNIE pipeline can now internally use the JASPAR database to import motifs and overlap them with peaks.Improve R packagehttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/12Vis update2022-07-05T09:13:58ZRim MoussaVis update- added layering options
- changed from returning NULL if nothing is plotted to returning GRN object- added layering options
- changed from returning NULL if nothing is plotted to returning GRN objecthttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/11minor changes2022-06-17T08:23:06ZRim Moussaminor changesupdated the getBackgroundGenes function.
- all_RNA as background: eliminated genes with 0 expression
- filtered_RNA as background: same as above but only include those in the filtered GRNupdated the getBackgroundGenes function.
- all_RNA as background: eliminated genes with 0 expression
- filtered_RNA as background: same as above but only include those in the filtered GRNhttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/10network visualization2022-06-17T08:24:02ZRim Moussanetwork visualizationhttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/9added new enrichment ontologies/databases2022-06-17T08:24:09ZRim Moussaadded new enrichment ontologies/databasesadded KEGG, Reactome, and Disease Ontology enrichmentsadded KEGG, Reactome, and Disease Ontology enrichmentshttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/8Documentation updates2021-11-16T21:07:29ZRim MoussaDocumentation updates- added examples to the documentation
- added biocViews tags
- added some imports to DESCRIPTION&NAMESPACE
- other minor changes suggested by `BiocCheck::BiocCheck()`
- remaining error left to handle: `Maintainer must add package name to...- added examples to the documentation
- added biocViews tags
- added some imports to DESCRIPTION&NAMESPACE
- other minor changes suggested by `BiocCheck::BiocCheck()`
- remaining error left to handle: `Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags.`https://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/7added tf-based enrichment + other minor changes to the commiunity enrichment ...2021-11-16T21:07:29ZRim Moussaadded tf-based enrichment + other minor changes to the commiunity enrichment and display- added a function to calculate TF enrichment (based on either degree centrality, eigenvector centrality, or a custom set of TFs)
- added a function to plot the TF enrichment
- added a function to retrieve top nodes
- if the user tries ...- added a function to calculate TF enrichment (based on either degree centrality, eigenvector centrality, or a custom set of TFs)
- added a function to plot the TF enrichment
- added a function to retrieve top nodes
- if the user tries to plot GO enrichment results for a TF or community for which the results haven't been previously calculated, they are automatically calculated in the plot function (with the default parameters).
- Enrichment is not calculated for all communities by defaulthttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/6added roxygen documentation to network summary functions2021-09-13T14:43:27ZRim Moussaadded roxygen documentation to network summary functionshttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/5added display for enrichment analysis2021-07-29T22:07:54ZRim Moussaadded display for enrichment analysisadded a heatmap that compares the top significantly enriched terms in the general enrichment to their p-value in community-based enrichment.added a heatmap that compares the top significantly enriched terms in the general enrichment to their p-value in community-based enrichment.https://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/4Import tf activity2021-07-27T20:32:07ZMaksim KholmatovImport tf activityhttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/3network structure summary + community analysis + enrichment analyses2021-07-26T11:36:41ZRim Moussanetwork structure summary + community analysis + enrichment analysesgeneral stats (vertex type distribution, degree distribution, central vertices)
community analysis (clustering using Louvain algorithm + general stats per community)
enrichment analysis (for the network and per community)general stats (vertex type distribution, degree distribution, central vertices)
community analysis (clustering using Louvain algorithm + general stats per community)
enrichment analysis (for the network and per community)https://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/2Return an error if consensus peaks overlap2021-05-17T20:02:46ZRim MoussaReturn an error if consensus peaks overlaphttps://git.embl.de/grp-zaugg/GRaNIE/-/merge_requests/1There's a cyclical dependency. checkmate is loaded by checkAndLoadPackages....2021-07-06T11:42:08ZMaksim KholmatovThere's a cyclical dependency. checkmate is loaded by checkAndLoadPackages....There's a cyclical dependency. checkmate is loaded by checkAndLoadPackages. But when it's called in all.R it also calls checkAndLoadPackagesGenomeAssembly to get additional arguments. Problem is checkAndLoadPackagesGenomeAssembly require...There's a cyclical dependency. checkmate is loaded by checkAndLoadPackages. But when it's called in all.R it also calls checkAndLoadPackagesGenomeAssembly to get additional arguments. Problem is checkAndLoadPackagesGenomeAssembly requires checkmate =)