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sheynkman-lab
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biosurfer
"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
MIT License
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Reimplement splice-aware isoform alignment
#57
jsaquing
closed
3 years ago
0
Add AminoAcid objects and link to corresponding Nucleotide objects
#56
jsaquing
closed
3 years ago
2
Design of groupings between objects?
#55
gsheynkman
closed
3 years ago
1
SQL database implentation of biosurfer
#54
bj8th
closed
3 years ago
0
Nomenclature - "frameshift"
#53
gsheynkman
closed
2 years ago
0
Nomenclature - "cut out splice"
#52
gsheynkman
closed
2 years ago
0
Nomenclature: Frameshift in the middle of the protein
#51
gsheynkman
closed
2 years ago
0
Naming of splicing that occurs internal to an exon
#50
gsheynkman
closed
2 years ago
0
Naming of split-codons associated with AAs
#49
gsheynkman
opened
3 years ago
0
Display isoform expression data
#48
gsheynkman
closed
3 years ago
4
Display disease mutations
#47
gsheynkman
opened
3 years ago
2
Show UTRs and CDSs by thickness
#46
gsheynkman
closed
3 years ago
1
Optimize isocreatealign
#45
jsaquing
closed
3 years ago
0
Selenocysteine codons incorrectly treated as stop codons
#44
jsaquing
opened
3 years ago
2
v2 isocreatealign code omits residues from certain genes
#43
jsaquing
closed
3 years ago
4
Representation of many, heterogeneous features linked to an ORF
#42
gsheynkman
opened
3 years ago
0
Python parallel - instantiation of gene objects, and alignment
#41
gsheynkman
closed
2 years ago
2
Time to instantiate gene object vs pickle load - profile
#40
gsheynkman
closed
3 years ago
2
How was “requirements.txt” populated?
#39
gsheynkman
closed
2 years ago
0
Dynamically set distance between isoform tracks
#38
gsheynkman
opened
3 years ago
0
Future - interactive isoform visualization?
#37
gsheynkman
opened
3 years ago
0
Display UTRs (thin bars) and CDS (thicker bars)
#36
gsheynkman
closed
3 years ago
1
Legend for figure elements
#35
gsheynkman
closed
3 years ago
0
Table to the y-axis labels
#34
gsheynkman
closed
3 years ago
0
APPRIS principles ORF marked
#33
gsheynkman
closed
2 years ago
0
Colored bars where start-methionine and stop codon are located on ORF
#32
gsheynkman
closed
3 years ago
0
Redundant domain creation in create_and_map_domain function
#31
gsheynkman
closed
3 years ago
1
Idea for optimizing feature representation
#30
gsheynkman
closed
3 years ago
1
Possibility - Expression class to describe the abundance of isoform and elements
#29
gsheynkman
opened
3 years ago
0
Annotation class to hold meta-data from databases (e.g., GO terms)
#28
gsheynkman
opened
3 years ago
0
Gloria cleanup biosurfer
#27
gsheynkman
closed
3 years ago
0
Implementation of disease mutation class
#26
gsheynkman
opened
3 years ago
1
Should isofunc.py and helpers.py be merged?
#25
gsheynkman
closed
3 years ago
0
Feature types to implement in biosurfer
#24
gsheynkman
opened
3 years ago
0
Features to implement for isoform plotting
#23
gsheynkman
closed
3 years ago
0
Ideas for encoding context and state-specific information
#22
gsheynkman
closed
2 years ago
2
Add transcripts and UTRs to isoclass hierarchy
#21
jsaquing
closed
3 years ago
7
annotating align blocks, improvements to IsoformPlot
#20
jsaquing
closed
3 years ago
0
How is the width of the y axis labels set in Isoplot.draw?
#19
gsheynkman
closed
3 years ago
2
Evaluate the necessity of outputting alignment group object during isoform plotting?
#18
gsheynkman
closed
3 years ago
1
Record and display whether GENCODE ORFs have "start/end not found" tags
#17
jsaquing
closed
3 years ago
0
fix subtle splicing detection/labeling code
#16
jsaquing
opened
3 years ago
0
How to deal with antisense transcripts
#15
gsheynkman
opened
3 years ago
0
replace magic constants/ints with Enums
#14
jsaquing
closed
3 years ago
2
Add type checking to other modules
#13
gsheynkman
opened
3 years ago
0
Reorganization of code - deleted irrelevant code parts.
#12
gsheynkman
closed
3 years ago
0
update IntegerInterval
#11
jsaquing
closed
3 years ago
0
Can BioCantor or a similar package be used to implement the iso-object hierarchy?
#10
jsaquing
closed
3 years ago
1
Enhance information in Alignment objects and their full string representations
#9
jsaquing
closed
3 years ago
3
merge "jared" into "main"
#8
jsaquing
closed
3 years ago
0
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