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goodarzilab
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pypage
python implementation of the PAGE algorithm
MIT License
15
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Differential gene set enrichment analysis
#49
abearab
opened
6 months ago
0
Option to assign single enrichment score instead of scores per bins
#48
abearab
opened
10 months ago
1
Error in `.filter_pathways` method
#47
abearab
opened
1 year ago
2
A method to draw heatmap from given enrichment score matrix
#46
abearab
opened
1 year ago
0
add method to extract `pvmatrix` like dataframe
#45
abearab
closed
1 year ago
1
Extract `pvmatrix` from pyPAGE run
#44
abearab
closed
1 year ago
2
manual link fixed
#43
artemy-bakulin
closed
1 year ago
0
Links to new repo in README
#42
artemy-bakulin
closed
1 year ago
0
Tested version
#41
artemy-bakulin
closed
1 year ago
0
Parallelization
#40
artemy-bakulin
opened
2 years ago
0
New discretization function
#39
artemy-bakulin
opened
2 years ago
3
Ipage2 merge
#38
noamteyssier
closed
2 years ago
0
Expose Heatmap kwargs to the user from PAGE.heatmap()
#37
noamteyssier
opened
2 years ago
2
Clean up the code in read annotation file in GeneOntology
#36
noamteyssier
opened
2 years ago
1
Exploring histogram binning for gene ontology data
#35
noamteyssier
opened
2 years ago
1
Generate Bins on ExpressionProfile after Finding Gene Intersection
#34
noamteyssier
opened
2 years ago
1
Merge ipage2 with pypage
#33
noamteyssier
closed
2 years ago
17
Updated version of pyPAGE
#32
artemy-bakulin
closed
2 years ago
0
fix print bug in expression object
#31
noamteyssier
opened
2 years ago
0
Introduce gene -> pathway mapping as a networkx object
#30
noamteyssier
opened
2 years ago
0
update readme with new self changes
#29
noamteyssier
opened
2 years ago
0
Return mutual information score in results table
#28
noamteyssier
closed
2 years ago
1
26 convert page object to operate on a single expression ontology object at a time
#27
noamteyssier
closed
2 years ago
0
convert `PAGE` object to operate on a single expression / ontology object at a time
#26
noamteyssier
closed
2 years ago
0
13 implement minmax pathway sizes in gene ontology
#25
noamteyssier
closed
2 years ago
1
23 change ontology input requirements to two vectors
#24
noamteyssier
closed
2 years ago
0
Change ontology input requirements to two vectors
#23
noamteyssier
closed
2 years ago
0
2 implement histogram binning on expression profile
#22
noamteyssier
closed
2 years ago
0
Keep a record of the pathways filtered and what pathway it was collapsed into
#21
noamteyssier
opened
2 years ago
0
Write up a command line interface
#20
noamteyssier
opened
2 years ago
0
Write up a tutorial for example usage
#19
noamteyssier
opened
2 years ago
1
5 write up a read the docs page
#18
noamteyssier
closed
2 years ago
0
14 clean up imports in api
#17
noamteyssier
closed
2 years ago
0
Entropy
#16
noamteyssier
closed
2 years ago
0
Validate correct MI and CMI
#15
noamteyssier
closed
2 years ago
0
Clean up imports in API
#14
noamteyssier
closed
2 years ago
0
Implement min/max pathway sizes in gene ontology
#13
noamteyssier
closed
2 years ago
1
Implement collapsing on gene homology
#12
noamteyssier
opened
2 years ago
0
Core limit
#11
noamteyssier
closed
2 years ago
0
Handle condition where no pathway indices pass informative criteria
#10
noamteyssier
closed
2 years ago
2
Set optional number of parallel threads with numba
#9
noamteyssier
closed
2 years ago
0
build up CMI from gene abundance with ipage2
#8
noamteyssier
closed
2 years ago
1
move histograms to seperate file
#7
noamteyssier
closed
2 years ago
0
CMI
#6
noamteyssier
closed
2 years ago
0
Write up a Read the Docs Page
#5
noamteyssier
closed
2 years ago
0
Optional Index / Expression Profile as Dataframe or File Path
#4
noamteyssier
closed
2 years ago
0
Implement Redundancy Trimming
#3
noamteyssier
closed
2 years ago
0
Implement Histogram Binning on Expression Profile
#2
noamteyssier
closed
2 years ago
0
Implement Conditional Mutual Information
#1
noamteyssier
closed
2 years ago
0