SRP-pipeline merge requestshttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests2022-06-10T09:28:16Zhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/38Add links to new StringDB databases2022-06-10T09:28:16ZPhilippe BORDRONAdd links to new StringDB databasesLink to new DB included into String
Tested successfully on TESTDATALink to new DB included into String
Tested successfully on TESTDATAEric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/37Update + Fix StringDB network display2022-06-07T07:21:18ZPhilippe BORDRONUpdate + Fix StringDB network display- Nodes display is now correct by deactivating the global v-align that was set to baseline
- Updated combined_embedded_network from v2.0.2 to v2.0.4
- Mod combined_embedded_network to allows to choose a divID
- Update make_html to manage...- Nodes display is now correct by deactivating the global v-align that was set to baseline
- Updated combined_embedded_network from v2.0.2 to v2.0.4
- Mod combined_embedded_network to allows to choose a divID
- Update make_html to manage 1 gene netwok that is a nonsenseEric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/36fix do.db dependency resolution with mamba2021-09-14T07:54:28ZPhilippe BORDRONfix do.db dependency resolution with mambaEnable mamba againEnable mamba againEric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/34Update according to StringDB changes2020-10-23T09:28:56ZPhilippe BORDRONUpdate according to StringDB changesEnrichment file returned by string has change a little and break some links in the report.
- This PR fix this problem.
- It also manage the NetworkNeighborAL terms.
- String now complete inputGenes in with no DE genes when only 1 DE gen...Enrichment file returned by string has change a little and break some links in the report.
- This PR fix this problem.
- It also manage the NetworkNeighborAL terms.
- String now complete inputGenes in with no DE genes when only 1 DE genes is queried. This PR fix this issue by coloring no DE genes in grey.Eric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/33Split reports2020-10-13T08:02:50ZPhilippe BORDRONSplit reportsSplit comparisons into many reports. The primary part is kept in each report.
The splitting is controlled through the comparison file.
For example, the `comparisons.tsv` with the following content will produce one main report `report.h...Split comparisons into many reports. The primary part is kept in each report.
The splitting is controlled through the comparison file.
For example, the `comparisons.tsv` with the following content will produce one main report `report.html` that will contains comparisons `cond1 vs cond2` and `cond1 vs cond3`, and an additional report `report-part2.html`that will contains comparison `cond2 vs cond3`.
```
TestProject cond1 cond2
TestProject cond1 cond3
TestProject::part2 cond2 cond3
```
The `::` part is the separator between project and report part. @eric.charpentier We can change it for something else.
Multiplate reports must use the 3 columns format for comparisons if multipart report is asked. The 2 columns format still valid if no mulipart report is asked. Project prefix can be omited like in the following example:
```
cond1 cond2
cond1 cond3
::part2 cond2 cond3
```Eric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/32Report cleanup2020-09-23T13:04:12ZPhilippe BORDRONReport cleanupRemove unused columns in html tablesRemove unused columns in html tablesPhilippe BORDRONPhilippe BORDRONhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/30De seq2 formula2020-10-13T08:13:03ZPhilippe BORDRONDe seq2 formula## Description
An hidden way that allow to ignore factors or/and plate effect if needed. User must know what he does when using it.
This is a proposal, so fell free to comment this PR (ping @eric.charpentier)
### How to use it
In order...## Description
An hidden way that allow to ignore factors or/and plate effect if needed. User must know what he does when using it.
This is a proposal, so fell free to comment this PR (ping @eric.charpentier)
### How to use it
In order to ignore factor or plate effect, user must add a `"normalizationOptions"` entry in the `comparisons` part of the project in the `config.json`. The entry must describes a list that contains `"--ignore-plate-effect"` or/and `"--ignore-batch-effect"`.
### Example:
```
{
...
"comparisons": {
"TestProject": {
...
"normalizationOptions" : ["--ignore-plate-effect"],
...
}
}
}
```Eric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/29Hovering pca2020-09-21T08:59:12ZPhilippe BORDRONHovering pcaDisplay sample id when hovering on dot in pca figure.Display sample id when hovering on dot in pca figure.Eric CHARPENTIEREric CHARPENTIERhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/28Display much conditions2020-09-09T14:08:07ZPhilippe BORDRONDisplay much conditionsWork on adaptive legend size in order to keep it in to picture while maintaining a correct plot surfaceWork on adaptive legend size in order to keep it in to picture while maintaining a correct plot surfacehttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/26Manage missing annot files2020-06-24T08:23:06ZPhilippe BORDRONManage missing annot filesI forgot to check if file exists before opening it. Now it is the caseI forgot to check if file exists before opening it. Now it is the casehttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/25fix inversed DE gene color2020-06-03T16:27:13ZPhilippe BORDRONfix inversed DE gene colorhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/24color gene FC according to its value2020-06-03T15:11:06ZPhilippe BORDRONcolor gene FC according to its valuehttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/23Add dataTable for GO & KEGG enrichments2020-06-03T12:46:16ZPhilippe BORDRONAdd dataTable for GO & KEGG enrichmentshttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/22fix https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/issue...2020-05-29T12:44:52ZPhilippe BORDRONfix https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/issues/17https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/21fix https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/issue...2020-05-29T12:45:25ZPhilippe BORDRONfix https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/issues/16https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/19Interactive graph2020-06-03T12:43:58ZPhilippe BORDRONInteractive graphAdd an interactive layer on MA and Volcano plots that gives gene names when hovering on dots on the graph (even for non-labeled genes).
MA plot and Volcano plots are vectorial now, it is then possible to copy text (in particular gene na...Add an interactive layer on MA and Volcano plots that gives gene names when hovering on dots on the graph (even for non-labeled genes).
MA plot and Volcano plots are vectorial now, it is then possible to copy text (in particular gene names) that is printed in the plots and plots scale with resizing the page.https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/18update MA-plot and volcano plot2020-03-24T15:04:27ZPhilippe BORDRONupdate MA-plot and volcano plotMake MA-plot and Volcano plot easier to readMake MA-plot and Volcano plot easier to readhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/17Refactor conda2019-11-22T13:49:49ZEric CHARPENTIERRefactor condahttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/16fix conda env file and library installation2019-06-26T11:46:05ZPhilippe BORDRONfix conda env file and library installationBecause conda is brokenBecause conda is brokenhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/merge_requests/15Fix dge.yml2019-05-03T10:18:13ZPhilippe BORDRONFix dge.ymlCorrect following error
```
ResolvePackageNotFound:
- matplotlib==2.2.3=py36h8e2386c_0
```Correct following error
```
ResolvePackageNotFound:
- matplotlib==2.2.3=py36h8e2386c_0
```