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25 Open 52 Closed
25 Open 52 Closed
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Issues list

Clean up imports and standardize how code accesses resources within project directory
#95 opened Nov 16, 2021 by jsaquing
@jsaquing
Wiki for Biosurfer Project documentation Improvements or additions to documentation
#94 opened Nov 14, 2021 by gsheynkman
@jsaquing
1
Behavior of linking Nucleotides to Residues is possibly counterintuitive design high-level design ideas, brainstorming
#92 opened Nov 4, 2021 by jsaquing
Abstract data structure to handle relationships among parent and children design high-level design ideas, brainstorming postponed This should be handled in the future, but is low priority right now
#91 opened Oct 13, 2021 by jsaquing
How to better organize different data sources design high-level design ideas, brainstorming enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#90 opened Oct 12, 2021 by jsaquing
Reference database initialization design high-level design ideas, brainstorming enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#89 opened Oct 6, 2021 by jsaquing
Refactoring/optimization of IsoformPlot design high-level design ideas, brainstorming plotting Related to plotting and visualization postponed This should be handled in the future, but is low priority right now
#88 opened Oct 5, 2021 by jsaquing
1
Refactor Exon to map against an association table between the transcript and exon tables design high-level design ideas, brainstorming postponed This should be handled in the future, but is low priority right now
#85 opened Sep 24, 2021 by jsaquing
2
ProteinAlignmentBlock should account for AA sequence matches enhancement New feature or request priority high priority (should be addressed within the week)
#84 opened Sep 23, 2021 by jsaquing
@jsaquing
1
sQTL representations in biosurfer design high-level design ideas, brainstorming
#73 opened Sep 11, 2021 by gsheynkman
@jsaquing
Associate expression data with Transcript/Junction/Exon objects design high-level design ideas, brainstorming enhancement New feature or request
#72 opened Sep 10, 2021 by jsaquing
@jsaquing
1
Detect experimentally sequenced transcripts that are subsets of other transcripts enhancement New feature or request
#59 opened Aug 16, 2021 by jsaquing
2
Naming of split-codons associated with AAs design high-level design ideas, brainstorming nomenclature New nomenclature related to bio-objects.
#49 opened Jul 23, 2021 by gsheynkman
Display disease mutations enhancement New feature or request plotting Related to plotting and visualization postponed This should be handled in the future, but is low priority right now
#47 opened Jul 23, 2021 by gsheynkman
2
Selenocysteine codons incorrectly treated as stop codons bug Something isn't working enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#44 opened Jul 22, 2021 by jsaquing
2
Representation of many, heterogeneous features linked to an ORF design high-level design ideas, brainstorming
#42 opened Jul 20, 2021 by gsheynkman
Dynamically set distance between isoform tracks enhancement New feature or request plotting Related to plotting and visualization
#38 opened Jul 20, 2021 by gsheynkman
Future - interactive isoform visualization? enhancement New feature or request plotting Related to plotting and visualization postponed This should be handled in the future, but is low priority right now
#37 opened Jul 20, 2021 by gsheynkman
Possibility - Expression class to describe the abundance of isoform and elements design high-level design ideas, brainstorming enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#29 opened Jul 20, 2021 by gsheynkman
Annotation class to hold meta-data from databases (e.g., GO terms) enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#28 opened Jul 20, 2021 by gsheynkman
Implementation of disease mutation class design high-level design ideas, brainstorming enhancement New feature or request postponed This should be handled in the future, but is low priority right now
#26 opened Jul 20, 2021 by gsheynkman
1
Feature types to implement in biosurfer design high-level design ideas, brainstorming enhancement New feature or request
#24 opened Jul 19, 2021 by gsheynkman
fix subtle splicing detection/labeling code bug Something isn't working plotting Related to plotting and visualization postponed This should be handled in the future, but is low priority right now
#16 opened Jul 16, 2021 by jsaquing
@jsaquing
How to deal with antisense transcripts design high-level design ideas, brainstorming postponed This should be handled in the future, but is low priority right now
#15 opened Jul 16, 2021 by gsheynkman
Add type checking to other modules enhancement New feature or request
#13 opened Jul 16, 2021 by gsheynkman
@jsaquing
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