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greenelab
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core-accessory-interactome
Investigating the functional relationship between P. aeruginosa core and accessory genes.
BSD 3-Clause "New" or "Revised" License
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Combine Figures S2 and S3
#63
ajlee21
closed
2 years ago
1
Manuscript revisions
#62
ajlee21
closed
2 years ago
1
Update figure 1
#61
ajlee21
closed
2 years ago
1
Add revisions based on reviewer comments
#60
ajlee21
closed
2 years ago
1
Additional exploration
#59
ajlee21
closed
2 years ago
2
Update figures for manuscript
#58
ajlee21
closed
2 years ago
2
Figure and readme updates
#57
ajlee21
closed
2 years ago
0
Update analysis based on co-authors comments
#56
ajlee21
closed
2 years ago
2
Update readme
#55
ajlee21
closed
2 years ago
0
Another analysis reun and update figure 1
#54
ajlee21
closed
2 years ago
1
Redo analysis using latest version of compendia
#53
ajlee21
closed
2 years ago
0
Update manuscript figures and fix distance calculation
#52
ajlee21
closed
2 years ago
1
Make draft manuscript figures
#51
ajlee21
closed
2 years ago
1
Update core-core and core-acc analyses
#50
ajlee21
closed
2 years ago
1
Refactor and redo analyses using SPELL correlation matrix
#49
ajlee21
closed
2 years ago
0
Compare SPELL vs counts correlation
#48
ajlee21
closed
2 years ago
0
Extend stability
#47
ajlee21
closed
2 years ago
0
Add scripts and analysis nbs from SOPHIE
#46
ajlee21
closed
2 years ago
1
Minor refactor
#45
ajlee21
closed
2 years ago
1
Add more exploratory analysis from discussion with collaborator
#44
ajlee21
closed
3 years ago
2
Refactor
#43
ajlee21
closed
3 years ago
0
Add analyses examining accessory genes
#42
ajlee21
closed
3 years ago
1
Create figures and data for Georgia's manuscript
#41
ajlee21
closed
3 years ago
0
Add enrichment analysis of modules
#40
ajlee21
closed
3 years ago
1
Minor refactor and quantify common DEG analysis
#39
ajlee21
closed
3 years ago
1
Lookup samples for Georgia's manuscript
#38
ajlee21
closed
3 years ago
1
Validate that correlation modules are biologically relevant
#37
ajlee21
closed
3 years ago
1
Get acc-acc modules and annotate
#36
ajlee21
closed
3 years ago
0
Add analysis to compare core-core modules across strains
#35
ajlee21
closed
3 years ago
2
Refactor to prepare for separate module analysis
#34
ajlee21
closed
3 years ago
0
Compare relationships using genome distance vs expression distance
#33
ajlee21
closed
3 years ago
2
Re-run analysis using new QCd data
#32
ajlee21
closed
3 years ago
0
common DEGs and core/acc annotations
#31
ajlee21
closed
3 years ago
0
Calculate module composition
#30
ajlee21
closed
3 years ago
0
Add community detection and random walk approaches
#29
ajlee21
closed
3 years ago
0
Update validation scripts
#28
ajlee21
closed
3 years ago
0
Update clustering scripts
#27
ajlee21
closed
3 years ago
4
Update threshold for compendia and reprocess
#26
ajlee21
closed
3 years ago
0
Apply correlation correction
#25
ajlee21
closed
3 years ago
0
Simplify network analysis
#24
ajlee21
closed
3 years ago
0
Network validation
#23
ajlee21
closed
3 years ago
1
Considerations for tuning network
#22
ajlee21
opened
3 years ago
0
Add network analysis
#21
ajlee21
closed
3 years ago
1
Bin samples using accessory gene expression
#20
ajlee21
closed
3 years ago
1
Create expression compendia based on mapping rates
#19
ajlee21
closed
3 years ago
1
Explore data
#18
ajlee21
closed
3 years ago
1
Quick reorganization
#17
ajlee21
closed
3 years ago
0
Add clustering analysis of accessory genes for PAO1 and PA14 compendia
#16
ajlee21
closed
3 years ago
2
Add exploratory analysis
#15
ajlee21
closed
3 years ago
1
Create phage+PAO1 reference genome
#14
ajlee21
closed
3 years ago
1
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