PHATE

PHATE copied to clipboard

Hello, I recently came across the T-PHATE algorithm you published. Regarding its implementation, I was wondering how did you interfere with the PHATE algorithm. As far as I understand, you...

apathanasiadis

MDS smacof n_jobs argument

1

Hi- I just noticed that even though [embed_mds](https://github.com/KrishnaswamyLab/PHATE/blob/master/Python/phate/mds.py#L157) accepts an n_jobs argument, it never gets passed to the [smacof wrapper](https://github.com/KrishnaswamyLab/PHATE/blob/master/Python/phate/mds.py#L97) ~defaulting to 1 each time. Is that a problem? Btw,...

choltz95

Be able to use minkowski metric with p < 1

2

**Describe the bug** It seems that PHATE supports minkowski metric for both mds and knn computations. So, I would like to use this metric with p= 0.3 for running experiments....

ivan-marroquin

**Describe the bug** With my input data, I get a SVD error computation about "array must not contain infs or NaNs" when I do fit_transform to reduce dimensionality of input...

ivan-marroquin

Hey guys, I'm trying to understand how to appropriately use MAGIC and PHATE for my analysis. When I perform dimensionality reduction with PCA/ UMAP after imputing gene counts, the data...

vravik

s_gd2 typeerror

13

``` TypeError Traceback (most recent call last) in 1 import phate ----> 2 Y = phate.PHATE(knn_dist='precomputed').fit_transform(A) /mnt/eider_environments/EiderPython/local/apollo/env/EiderPython/python3.7/lib/python3.7/site-packages/phate/phate.py in fit_transform(self, X, **kwargs) 939 with _logger.task("PHATE"): 940 self.fit(X) --> 941 embedding =...

scottgigante

Hi, first off, great algorithm! I've used PHATE in my own work with very encouraging results and appreciate its clarity in studying continuous biological processes versus the more conventional tools...

jashahir

Totally different result between phateR and RunPHATE

2

Hi, I recently tried to run the EB differentiation PHATE tutorial. The tutorial is run in python, but I am more used to R, so I tried to run using...

qiuhuiqq

confront problems in using phateR

4

Hi, phateR team. I installed the phateR packge in HPC following 'Installation from CRAN and PyPi' steps as: ``` pip install --user phate install.packages("phateR") ``` There was no error in...

Shawn10312

HML 9:57 AM Hello- I first want to say how impressed I am with the PHATE method! I was really excited when I came across the method a few months...

scottgigante