alevax pyviper issues - Githubissues

alevax / pyviper

Porting of Protein Activity and Pathway Inference to single cell and Python.

MIT License

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Add SCENIC network loading tutorial to pyVIPER documentation

#83 alexanderlewis99 opened 2 days ago
1
remove incomptability issue with pandas 2.x.x

#82 LucaZanella15 opened 2 weeks ago
0
Fancier Docstrings

#81 alexanderlewis99 opened 2 weeks ago
0
No duplicate names allowed in metacell function

#80 alexanderlewis99 opened 3 weeks ago
0
Add warning/error when loading interacome if duplicate regulator --> target pairs

#79 alexanderlewis99 opened 3 weeks ago
0
wrapper for aracne or scenic to regulon

#78 LucaZanella15 opened 3 weeks ago
0
Default behavior of pyviper.tl.pca

#77 LucaZanella15 closed 3 weeks ago
0
network integration returns an error

#76 LucaZanella15 closed 3 weeks ago
1
Issue with NaRnEA and cell names with same ID

#75 LucaZanella15 opened 4 weeks ago
0
Compare SCENIC via pyVIPER versus ARACNe via pyVIPER

#74 alexanderlewis99 opened 4 weeks ago
0
Add an option to create the standard gSEA/aREA single regulator score/p-value plots

#73 alexanderlewis99 opened 1 month ago
0
Compatibility with NA input values

#72 alexanderlewis99 opened 1 month ago
0
Add lab network collection after their publication

#71 alexanderlewis99 opened 1 month ago
1
Use BioMarT database to classify genes as protein coding or non-protein coding

#70 alexanderlewis99 opened 1 month ago
0
Update repr_metacells to work when perc_data_to_use > 85

#69 alexanderlewis99 opened 2 months ago
0
NaRnEA Version of OncoMatch

#68 alexanderlewis99 opened 2 months ago
1
Update norm.cdf to scipy special for faster computation

#67 alexanderlewis99 opened 2 months ago
0
Add a tutorial 4 on OncoMatch

#66 alexanderlewis99 opened 2 months ago
0
Remove AnnData FutureWarning

#65 alexanderlewis99 closed 2 months ago
1
Check if we can call the underlying function behind scipy.stats.norm.cdf

#64 alexanderlewis99 closed 2 months ago
2
Add del functions to NaRnEA_classic to delete unneeded objects & free up memory

#63 alexanderlewis99 opened 2 months ago
1
Aligning cells in clusters Stouffer function

#62 alexanderlewis99 opened 2 months ago
0
To Do List

#61 alexanderlewis99 opened 3 months ago
2
Link to ARACNe3 GitHub Repository in Tutorial 3

#60 alexanderlewis99 opened 3 months ago
0
Add plot.msviper to the pyVIPER package

#59 alexanderlewis99 opened 3 months ago
0
ViperSimilarity but instead of being based on aREA, it should be based on NaRnEA

#58 alexanderlewis99 opened 3 months ago
1
Update pyviper network matching to use np.nan instead of 0?

#57 alexanderlewis99 opened 7 months ago
0
Update the translation code to handle multiple matches in either direction (forwards or backwards) with Aziz' new CSV

#56 alexanderlewis99 closed 3 months ago
1
Network assignment improvements

#55 alexanderlewis99 opened 7 months ago
0
Check lists of TFs/CoTFs

#54 alexanderlewis99 opened 7 months ago
0
make sure human2mouse.csv contains everything in human_genes.csv so we can be efficient

#53 alexanderlewis99 closed 3 months ago
2
Add translation function: input a list, output a list

#52 alexanderlewis99 closed 3 months ago
1
Update the current translation lists to all 30K known genes (symbol, ensembl, entrez)

#51 alexanderlewis99 closed 3 months ago
1
Reset batch sizes

#50 alexanderlewis99 closed 7 months ago
1
Add verbose so that many Interacome methods displays information:

#49 alexanderlewis99 closed 7 months ago
1
network assignment in viper as input

#48 LucaZanella15 closed 7 months ago
3
tfs-cotfs choice in Tutorial 2

#47 LucaZanella15 opened 8 months ago
0
Describe parameters and test aracne3_to_regulon in pp module

#46 LucaZanella15 opened 8 months ago
0
Add progress bars on pyther.viper when njobs = 1

#45 alexanderlewis99 opened 8 months ago
0
Figure out if PES can be used with OncoMatch

#44 alexanderlewis99 opened 8 months ago
0
Test tl.nes_to_pvalues

#43 LucaZanella15 opened 8 months ago
0
fix parallelization viper function

#42 LucaZanella15 closed 8 months ago
2
features in tl module

#41 LucaZanella15 opened 8 months ago
0
Add code to check the max # of cores

#40 alexanderlewis99 closed 8 months ago
1
Add ViperSimilarity

#39 alexanderlewis99 closed 8 months ago
1
Add OncoMatch

#38 alexanderlewis99 closed 8 months ago
1
Add PES calculated from VIPER NES

#37 alexanderlewis99 closed 8 months ago
1
Bugfix: filter_by_feature_groups=None

#36 alexanderlewis99 closed 3 months ago
1
Check if we should keep pyviper.tl.umap

#35 alexanderlewis99 closed 8 months ago
1
Get in touch with Scanpy to add Pyther to their shared documentation

#34 alexanderlewis99 opened 8 months ago
0