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License: Other
An application for exploring and visualizing differential gene expression data created with DESeq2
License: Other
In GitLab by @[email protected] on Nov 15, 2018, 14:19
Ascending should be descending and vice versa.
Ascending = 1,2,3,4,5
Descending = 5,4,3,2,1
In GitLab by @[email protected] on Apr 16, 2019, 10:27
For some reason, the download button on each top 10 plot has fewer options than other scatter plots (i.e. volcano plot)
In GitLab by @[email protected] on Mar 21, 2018, 17:27
Merges volcano_plot -> development
First functioning version of volcano plot
The original issue
Id: 19
Title: Does not update subset if subset is currently selected
could not be created.
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TODO
In GitLab by @[email protected] on Mar 28, 2018, 14:53
MA plot for DESeq2 data
In GitLab by @[email protected] on Aug 27, 2018, 10:34
Merges deseq2_overview_2 -> development
In GitLab by @[email protected] on Aug 10, 2018, 13:10
Merges deseq2_overview_2 -> development
The original issue
Id: 17
Title: Histograms for count data
could not be created.
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TODO
In GitLab by @[email protected] on Jul 3, 2018, 13:18
Each tab has a separate store at the moment.
Possible solutions:
In GitLab by @jwinter on Aug 31, 2018, 12:32
Merges deseq2_overview_2 -> development
Removed old code, added the column-memory-function at deseq2-overview.
The original issue
Id: 18
Title: Replace Set by Array for normalizationMethods in Dge
could not be created.
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TODO
In GitLab by @[email protected] on Mar 29, 2018, 17:02
Heat map with gene against sample and the read count visualized with the heat map color
The original issue
Id: 6
Title: Integration of raw data
could not be created.
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TODO
In GitLab by @mmueller on Apr 15, 2019, 09:26
"webpack": "^4.20.2"
"webpack-cli": "^3.1.1"
then ran npm install --save webpack-cli
-> other versions of webpack and webpack-cli not necessary, but the npm install --save webpack-cli seems to be.
The original issue
Id: 2
Title: check conditions to be valid in file uploader
could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:
TODO
In GitLab by @[email protected] on Mar 28, 2019, 12:46
The "Reset Table" button in DESeq2 Overview does not reset the table completely. After setting a filter in one column and then resetting the table, the filter is still active (only the icon is gone).
In GitLab by @[email protected] on Apr 10, 2018, 14:51
Create a range slider with a customizable gradient background as vue component. It can be used to select the intermediate color stop in heat maps. The value of this slider should be mirrored as the center of the gradient.
https://stackoverflow.com/questions/48985608/change-color-gradient-of-input-slider-using-js?rq=1 can be used as a template.
In GitLab by @[email protected] on Mar 13, 2018, 12:44
There should be a way to reset/empty the dge object. This includes frontend work and adding new actions and mutations to the vuex store.
In GitLab by @[email protected] on Mar 18, 2020, 11:31
An additional header including the conditions of each column would make the overview table user-friendlier
In GitLab by @jwinter on Mar 8, 2018, 14:01
Merges patch-1 -> master
In GitLab by @mmueller on Apr 15, 2019, 13:16
upload of deseq2_results (e.g. _t0_Vs._t1_large.csv) results in gene_0 missing in store
.csv has 1Mio entries (starting with gene_0)
DGE store says: 999.999 genes, starting with gene_1
In GitLab by @rmueller on Jun 12, 2018, 17:28
In GitLab by @[email protected] on Mar 10, 2018, 17:29
Merges jest_integration -> development
Jest is integrated and tests for dge.js were added
In GitLab by @[email protected] on Jul 17, 2018, 13:33
A lot of warnings appear on the web console if "Deseq2 overview" is opened with the test data.
ag-grid: invalid gridOptions property 'ob' did you mean any of these:
groupSuppressBlankHeader,slaveGrids,rowData,columnDefs,excelStyles,pinnedTopRowData,pinnedBottomRowData,components
gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid gridOptions properties please check: https://www.ag-grid.com/javascript-grid-properties/
gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent
gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132
gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent
gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132
gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent
gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
GridOptionsWrapper.checkProperties @ gridOptionsWrapper.js?6987:132
gridOptionsWrapper.js?6987:129 ag-grid: invalid colDef property 'ob' did you mean any of these: rowGroupIndex,children,allowedAggFuncs,menuTabs,pivotTotalColumnIds,cellClassRules,icons,headerGroupComponent
gridOptionsWrapper.js?6987:132 ag-grid: to see all the valid colDef properties please check: https://www.ag-grid.com/javascript-grid-column-properties/
In GitLab by @jwinter on Jun 20, 2018, 13:23
Merges deseq2_overview_2 -> development
Ready to merge.
In GitLab by @[email protected] on Apr 17, 2019, 16:29
DESeq2 Top10 and Overview must get newly formatted since new ESLint update caused many warnings and errors
In GitLab by @[email protected] on Apr 24, 2018, 20:23
Chart export cannot be recognized as images (see attachment visualizer_heatmap_03)
In GitLab by @[email protected] on Mar 13, 2018, 12:23
The conditions of a analysis could be guessed with the file name.
In GitLab by @[email protected] on Mar 28, 2018, 13:27
Merges raw_data_integration -> development
add a raw version of feature #6
In GitLab by @jwinter on Aug 27, 2018, 15:14
Merges deseq2_overview_2 -> development
In GitLab by @[email protected] on Mar 28, 2019, 11:48
Gene names are bigger than their surrounding box in "Current subset" box. The surrounding box should grow with the name length.
In GitLab by @jwinter on Aug 27, 2018, 11:49
Merges top10_genes -> development
In GitLab by @[email protected] on Mar 28, 2018, 13:35
A visualization of the most significant genes (Top 10?).
In GitLab by @[email protected] on Jul 17, 2018, 13:15
Added non-passive event listener to a scroll-blocking 'mousewheel' event. Consider marking event handler as 'passive' to make the page more responsive.
In GitLab by @jwinter on Jul 12, 2018, 10:48
Merges deseq2_overview_2 -> development
In GitLab by @[email protected] on Nov 15, 2018, 14:13
There should be some kind of button to add a gene to the subset.
Button? Link?
The original issue
Id: 21
Title: p-Value histogram
could not be created.
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TODO
The original issue
Id: 26
Title: counts vs. counts scatter plot
could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:
TODO
The original issue
Id: 22
Title: log2 fold change histogram
could not be created.
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TODO
In GitLab by @[email protected] on Apr 6, 2018, 14:40
Merges tidy_up_webpack -> development
merging for testing ci-runner
In GitLab by @mmueller on Aug 8, 2019, 10:56
Metadata and DESeq2 data are merged based on full feature IDs. If the IDs do not match fully, import for a gff will be blocked. Might lead to problems, if the user changed IDs during data processing (featureCounts, gff).
The original issue
Id: 27
Title: Import of multiple count tables
could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:
TODO
In GitLab by @jwinter on Jul 22, 2018, 14:29
Merges deseq2_overview_2 -> development
Folgendes wurde in den letzten Tagen geaddet:
The original issue
Id: 13
Title: Exchange volcano plot series for highcharts zones
could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:
TODO
In GitLab by @[email protected] on Mar 28, 2019, 12:53
In GitLab by @jwinter on Aug 5, 2018, 11:10
Merges deseq2_overview_2 -> development
DESeq2_overview_2 müsste fertig sein. Zu beachten wäre, dass du an anderer Stelle schon die Farben der Balken geändert hast (DESeq2_Overview, Tabelle, Log2FoldChange).
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