sheynkman-lab biosurfer issues

sheynkman-lab / 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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updated READE.md

#107 MayankMurali closed 1 year ago
0
Merging dev to main for first version release

#106 MayankMurali closed 1 year ago
0
update genome wide alignment analysis script

#105 jsaquing closed 1 year ago
0
Plot update merging to dev

#104 MayankMurali closed 1 year ago
0
Hybrid-alignment summary added

#103 jsaquing closed 1 year ago
0
implementing plotting CLI

#102 jsaquing closed 1 year ago
0
Genome-wide p-block classification and analysis

#101 jsaquing closed 2 years ago
0
Redesign of hybrid alignment system

#100 jsaquing closed 2 years ago
0
initial database creation

#99 bj8th closed 6 months ago
0
Frameshifts are reversed for minus strand genes

#98 jsaquing closed 2 years ago
0
December-January miscellany

#97 jsaquing closed 2 years ago
0
Implement basic protein feature representation, plotting, and analysis

#96 jsaquing closed 2 years ago
0
Clean up imports and standardize how code accesses resources within project directory

#95 jsaquing opened 2 years ago
0
Wiki for Biosurfer Project

#94 gsheynkman opened 2 years ago
1
Annotation primitives as objects themselves

#93 gsheynkman closed 2 years ago
2
Behavior of linking Nucleotides to Residues is possibly counterintuitive

#92 jsaquing opened 2 years ago
0
Abstract data structure to handle relationships among parent and children

#91 jsaquing opened 2 years ago
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How to better organize different data sources

#90 jsaquing opened 2 years ago
0
Reference database initialization

#89 jsaquing opened 2 years ago
0
Refactoring/optimization of IsoformPlot

#88 jsaquing opened 2 years ago
1
Implement testing with hypothesis

#87 jsaquing closed 3 years ago
0
Resolving overlaps between domain mappings

#86 jsaquing closed 2 years ago
2
Refactor Exon to map against an association table between the transcript and exon tables

#85 jsaquing opened 3 years ago
2
ProteinAlignmentBlock should account for AA sequence matches

#84 jsaquing opened 3 years ago
1
Create Database class and restructure tests directory

#83 jsaquing closed 3 years ago
0
ORF start/stop location in transript bug

#82 bj8th closed 2 years ago
3
update variant

#81 bj8th closed 3 years ago
0
Start implementing tests

#80 jsaquing closed 3 years ago
0
Implement generic ProteinFeature class

#79 jsaquing closed 2 years ago
0
EXITC detection raises error when aligning some transcripts

#78 jsaquing closed 2 years ago
0
Display "absolute" frame of translation instead of relative

#77 jsaquing closed 2 years ago
1
Gene-row track for expression visualization

#76 gsheynkman closed 2 years ago
0
load PacBio data and perform sQTL analysis

#75 jsaquing closed 3 years ago
0
Associate novelty information for PacBio transcripts read into Biosurfer

#74 gsheynkman closed 3 years ago
0
sQTL representations in biosurfer

#73 gsheynkman opened 3 years ago
0
Associate expression data with Transcript/Junction/Exon objects

#72 jsaquing opened 3 years ago
1
Load objects from LRP pipeline output

#71 jsaquing closed 3 years ago
0
Implement prototype sQTL analysis

#70 jsaquing closed 3 years ago
0
overhauling alignment event classification and annotation

#69 jsaquing closed 2 years ago
1
Create a schematic for every base_annotation category (in SVG file)

#68 gsheynkman closed 2 years ago
0
update headers

#67 gsheynkman closed 2 years ago
0
Implement sQTL analysis

#66 jsaquing closed 3 years ago
1
Restructure directories

#65 jsaquing closed 3 years ago
0
Database querying is a bit slow (especially for Transcript)

#64 jsaquing closed 3 years ago
1
Refactor database

#63 jsaquing closed 3 years ago
0
Reimplement plotting

#62 jsaquing closed 3 years ago
0
Need a word that represents new exon sequence that harbors a start codon...

#61 gsheynkman closed 2 years ago
0
Word for alternative 5' end with/without start codon

#60 gsheynkman closed 3 years ago
2
Detect experimentally sequenced transcripts that are subsets of other transcripts

#59 jsaquing opened 3 years ago
2
Reimplement splice-based alignments

#58 jsaquing closed 3 years ago
0