claassenlab/Teamproject-2023

Implementation of RNA velocity for estimation of single cell transcriptomic dynamics.

Python

Issues

Analysis on unspliced proportions
#68 opened a year ago by RTapiaSE
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As a user I want to display the gene velocities as a phase plot
#51 opened a year ago by Raffael-Rack
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As a user I want to display the data as a stream plot
#39 opened a year ago by Raffael-Rack
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Fix velocity graph bug
#81 opened a year ago by FinnSpr
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As a user want to overlay the single cell velocities over the UMAP projection
#40 opened a year ago by Raffael-Rack
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As a user I want to compute velocity estimates
#62 opened a year ago by Raffael-Rack
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As a user I want to know which and how many genes are usable for velocity analysis
#64 opened a year ago by Raffael-Rack
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As a user I want to have an output of the velocity gene list and the criteria for their choice.
#52 opened a year ago by Raffael-Rack
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Improve understandability of data overview
#78 opened a year ago by FinnSpr
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As a user I want a statistical evaluation of the velocities
#61 opened a year ago by Raffael-Rack
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Velocity variability in a certain region
#77 opened a year ago by FinnSpr
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As a user I want to display multiple visualizations of different types at the same time
#37 opened a year ago by Raffael-Rack
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As a user I want to display the velocities as a box plot
#36 opened a year ago by Raffael-Rack
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As user I want to output the underlying data in tabular form
#50 opened a year ago by Raffael-Rack
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As a user I want to know how well the model assumptions hold
#63 opened a year ago by Raffael-Rack
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As a user I want to know the regression loss of a visualization
#45 opened a year ago by Raffael-Rack
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As a user I want to know the likelihood of each visualization.
#43 opened a year ago by Raffael-Rack
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As a user I want to know the confidence interval of a visualization
#44 opened a year ago by Raffael-Rack
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As a user I want to display multiple of the same visualization with different parameters.
#38 opened a year ago by Raffael-Rack
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As a user I want to group clusters in the visualization together, for a better overview
#42 opened a year ago by Raffael-Rack
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As a user I want a velocity field based analysis
#60 opened a year ago by Raffael-Rack
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As a user I want to identify clusters and their velocity
#59 opened a year ago by Raffael-Rack
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As a user I want to output the model parameters in tabular form
#48 opened a year ago by Raffael-Rack
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As a user I want to run a velocyto model
#46 opened a year ago by Raffael-Rack
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As a user I want to run a scvelo model
#47 opened a year ago by Raffael-Rack
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As a user I want to export my visualization as a pdf
#53 opened a year ago by Raffael-Rack
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As a user I want to export my visualization as an image
#54 opened a year ago by Raffael-Rack
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As a user I want to analyze pseudotime
#58 opened a year ago by Raffael-Rack
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As a user I want to be able to save an analysis
#56 opened a year ago by Raffael-Rack
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As a user I want to be able to load an analysis
#57 opened a year ago by Raffael-Rack
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As a user I want to export my analysis settings
#55 opened a year ago by Raffael-Rack
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Convert BAM file to Loom file
#32 opened a year ago by Raffael-Rack
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Convert FastQ file to Loom file
#33 opened a year ago by Raffael-Rack
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PCA-Visualization Plot
#69 opened a year ago by RTapiaSE
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Find the cells with max/min number of non-zero signal genes.
#26 opened a year ago by Raffael-Rack
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Increase the efficiency of the basic overview.
#74 opened a year ago by Raffael-Rack
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Determine the average amount of non-zero signal genes.
#28 opened a year ago by Raffael-Rack
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Fix loading panel
#70 opened a year ago by FinnSpr
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As a user I want to have a UMAP projection of the single-cell transcriptomic data
#41 opened a year ago by Raffael-Rack
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Loading panel for data overview and run analysis
#66 opened a year ago by FinnSpr
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Write dataset overview to a txt file
#65 opened a year ago by FinnSpr
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As a user I want to save visualizations as a PDF.
#49 opened a year ago by Raffael-Rack
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Display the basic overview information.
#30 opened a year ago by Raffael-Rack
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Ensure readability of the Tooltip in a device on dark Mode
#35 opened a year ago by RTapiaSE
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Get the number of genes in the data.
#24 opened a year ago by Raffael-Rack
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Determine the amount of cells in the provided data.
#22 opened a year ago by Raffael-Rack
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Determine the average amount of non-zero signal genes. (FastQ files)
#29 opened a year ago by Raffael-Rack
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Find the cells with max/min number of non-zero signal genes. (FastQ file)
#27 opened a year ago by Raffael-Rack
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Get the number of genes in the data. (FastQ File)
#25 opened a year ago by Raffael-Rack
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Determine the amount of cells in the provided data (FastQ File)
#23 opened a year ago by Raffael-Rack
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