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alevax
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pyviper
Porting of Protein Activity and Pathway Inference to single cell and Python.
MIT License
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network assignment in viper as input
#48
LucaZanella15
closed
10 months ago
3
tfs-cotfs choice in Tutorial 2
#47
LucaZanella15
opened
11 months ago
0
Describe parameters and test aracne3_to_regulon in pp module
#46
LucaZanella15
opened
11 months ago
0
Add progress bars on pyther.viper when njobs = 1
#45
alexanderlewis99
opened
11 months ago
0
Figure out if PES can be used with OncoMatch
#44
alexanderlewis99
opened
11 months ago
0
Test tl.nes_to_pvalues
#43
LucaZanella15
opened
11 months ago
0
fix parallelization viper function
#42
LucaZanella15
closed
11 months ago
2
features in tl module
#41
LucaZanella15
opened
11 months ago
0
Add code to check the max # of cores
#40
alexanderlewis99
closed
11 months ago
1
Add ViperSimilarity
#39
alexanderlewis99
closed
11 months ago
1
Add OncoMatch
#38
alexanderlewis99
closed
11 months ago
1
Add PES calculated from VIPER NES
#37
alexanderlewis99
closed
11 months ago
1
Bugfix: filter_by_feature_groups=None
#36
alexanderlewis99
closed
6 months ago
1
Check if we should keep pyviper.tl.umap
#35
alexanderlewis99
closed
11 months ago
1
Get in touch with Scanpy to add Pyther to their shared documentation
#34
alexanderlewis99
opened
11 months ago
0
In config: add option to add one's own translate DF
#33
alexanderlewis99
opened
12 months ago
0
Filter by group method for Interactome class.
#32
alexanderlewis99
closed
12 months ago
1
Combine path_enr and pyther
#31
alexanderlewis99
closed
12 months ago
1
Add entrez gene format to translate functions
#30
alexanderlewis99
closed
11 months ago
0
Add translate method to Interactome class
#29
alexanderlewis99
closed
12 months ago
1
Merge Pyther v2 beta into main branch
#28
alexanderlewis99
closed
12 months ago
1
Create a ReadTheDocs.io
#27
alexanderlewis99
closed
11 months ago
1
Update path_enr to work with either aREA or NaRnEA
#26
alexanderlewis99
closed
12 months ago
1
Switch data storage slot in Anndata
#25
alexanderlewis99
closed
1 year ago
1
Where to include data for test in Notebook
#24
LucaZanella15
closed
11 months ago
1
Update readme, clean codebase from useless files and migrate to Califano Lab when ready
#23
LucaZanella15
opened
1 year ago
0
NaRnEA sample_weight parameter has no purpose. What was it supposed to do?
#22
alexanderlewis99
closed
11 months ago
2
Later after ACDC-small is published, include ACDC in the jupyter notebook walkthrough for the clustering
#21
alexanderlewis99
opened
1 year ago
0
Check whether method="rank" in Pyther should result in our custom rank_norm function being used
#20
alexanderlewis99
closed
11 months ago
2
Small bug - if you provide 2 identical networks to NaRnEA it causes an error
#19
alexanderlewis99
closed
11 months ago
1
Add adaptive to Interactome.prune - make this pruneRegulon function the same as VIPER's
#18
alexanderlewis99
closed
11 months ago
2
Convert data in pyther/data from .tsv/.txt/.csv to .pkl for faster loading
#17
alexanderlewis99
closed
11 months ago
1
Speed up everything by switching from pandas DataFrames to numpy for mathematical operations
#16
alexanderlewis99
opened
1 year ago
0
See if we can use multicore with a single aREA/NaRnEA run by slicing the data
#15
alexanderlewis99
closed
11 months ago
2
Can we do meta_aREA without using a long data format? Is this possible?
#14
alexanderlewis99
closed
1 year ago
2
Modify Pyther so that when njobs = 1, don't use any Parallel; run aREA (not meta_aREA) when using 1 network only
#13
alexanderlewis99
closed
1 year ago
1
1 jupyter notebook as a "demo" for a use case of pathway enrichment & translation functions
#12
alexanderlewis99
closed
11 months ago
0
Fix NaRneA numerical approximation of qnorm in the function
#11
alevax
closed
1 year ago
1
Merge matrix_narnea and meta_narnea into one wrapped called narnea
#10
alevax
closed
1 year ago
1
Fix loading time (very slow) of network import, function load_network()
#9
alevax
closed
1 year ago
1
Create pathway enrichment function to be compatible with MSigDB gene sets and scanpy annData
#8
alevax
closed
1 year ago
1
Pyther v2 beta
#7
zl3263
closed
1 year ago
0
allow slice_compute_combine for computation
#6
zl3263
closed
1 year ago
1
incredibly slow when using `load_interactome_from`
#5
zl3263
closed
1 year ago
1
README with straightforward example
#4
LucaZanella15
closed
11 months ago
0
matrix_narnea with arrays
#3
LucaZanella15
closed
1 year ago
1
make the output consistent in type with input by default.
#2
zl3263
closed
11 months ago
0
Put back the `layer` in pyther funtion
#1
zl3263
closed
1 year ago
1
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