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sjteresi
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Blueberry_Network_Rewiring
Code and documentation for the "Blueberry Galling Project". Part of my second thesis chapter
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Refactor Makefile to have more cohesive input/output path
#89
sjteresi
closed
5 months ago
0
Refactor Makefile to have more cohesive input/output path
#88
sjteresi
closed
1 year ago
0
Add TopGO code for DEGs, add doc to analyses
#87
sjteresi
closed
1 year ago
0
Remove old summary table
#86
sjteresi
closed
1 year ago
0
Recreate QTL table to include genes missed by collaborators
#85
sjteresi
closed
1 year ago
1
Add simple analysis of QTL genes that are DEGs
#84
sjteresi
closed
1 year ago
0
Add linegraphs of expression of genes per module
#83
sjteresi
closed
1 year ago
0
Get counts of DEGs with and without orthologs
#82
sjteresi
closed
1 year ago
0
Provide updated DEG and module table for analysis
#81
sjteresi
closed
2 years ago
0
F/important modules and go
#80
sjteresi
closed
2 years ago
0
Removed the code to generate the log2fc histogram.
#79
Alder-pixel
closed
2 years ago
0
F/melanie module table
#78
sjteresi
closed
2 years ago
0
Add protein table to filtration to make things easier for Melanie
#77
sjteresi
closed
2 years ago
0
F/refactor deg go mod
#76
sjteresi
closed
2 years ago
0
Add code to output tables of genes to accompany venn diagrams
#75
sjteresi
closed
2 years ago
0
Remove uninformative rows and columns
#74
sjteresi
closed
2 years ago
0
Add venn diagrams to DEG code, tracking DEG overlap between genotypes over time
#73
sjteresi
closed
2 years ago
0
Better merge/concat code so that the output table does not have confusing column suffixes
#72
sjteresi
closed
2 years ago
0
Add code to make line plot of DEGS per context
#71
sjteresi
closed
2 years ago
0
Determine GO term overlap with modules using Melanie's list
#70
sjteresi
closed
2 years ago
0
Add overlap with module code. Determine what Log2FC genes and DEGs ar…
#69
sjteresi
closed
2 years ago
0
Determine overlap of modules and Log2FC genes
#68
sjteresi
closed
2 years ago
0
F/module log2fc histogram
#67
Alder-pixel
closed
2 years ago
0
F/module deg table
#66
sjteresi
closed
2 years ago
0
F/log2fc analysis
#65
sjteresi
closed
2 years ago
0
Explore options of exporting WGCNA data to Cytoscape
#64
sjteresi
closed
2 years ago
1
Create table of module ID and # of differentially expressed genes
#63
sjteresi
closed
2 years ago
4
README Documentation Update
#62
sjteresi
closed
2 years ago
1
Delete gene_stats / operations.py
#61
Alder-pixel
closed
2 years ago
0
Overhaul README
#60
sjteresi
closed
2 years ago
0
Add the TopGO overrepresentation data to summary table
#59
sjteresi
closed
2 years ago
1
Bring back filter modules and add doc to TopGO
#58
sjteresi
closed
2 years ago
0
WGCNA Documentation Incomplete
#57
sjteresi
closed
2 years ago
2
Provide more documentation on TopGO related scripts
#56
sjteresi
closed
2 years ago
1
D/54 filter modules doc
#55
sjteresi
closed
2 years ago
0
Edit filter_modules.py to have appropriate input/output paths and provide greater documentation.
#54
sjteresi
closed
2 years ago
0
D/52 fpkm tpm
#53
sjteresi
closed
2 years ago
0
Add Makefile information and more documentation for FPKM/TPM Code
#52
sjteresi
closed
2 years ago
0
Remove old unused analysis code and redirect output to more appropria…
#51
sjteresi
closed
2 years ago
0
Add documentation about E-value sorting and dropping of duplicates
#50
sjteresi
closed
2 years ago
0
Verify choosing the best (least) E-Value in the homology/synteny code is correct
#49
sjteresi
closed
2 years ago
0
Remove unused AT_BB Union Code and reorganize output of AT_BB section
#48
sjteresi
closed
2 years ago
0
All-Encompassing Summary Table Does Not Have The Total No. of Genes
#47
sjteresi
closed
2 years ago
1
Add more documentation to WGCNA and remove old unused test code
#46
sjteresi
closed
2 years ago
0
Remove extraneous code from WGCNA script
#45
sjteresi
closed
2 years ago
0
Rename scripts directory to src and change required code in files to …
#44
sjteresi
closed
2 years ago
0
Rename script directory to src and change code files accordingly
#43
sjteresi
closed
2 years ago
0
F/master table
#42
sjteresi
closed
2 years ago
0
Delete diff_ex_table code (python and makefile)
#41
sjteresi
closed
2 years ago
0
Add TopGO script creating summary table and graphic for each module
#40
sjteresi
closed
2 years ago
0
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