Shobi Stassen

i am finding that during stage two my CPUs are used in parallel in a periodic manner. If this stage is not parallelized, why do I see this kind of...

@vasturiano Thanks so much, your fix for 1) and 2) works perfectly. For item 3, if I use your code to modify the repulsion strength (even to -10 all the...

@shijianasdf hi did you managed to solve this issue, I also get the EOF error

I also wanted to add that the initial filtering and normalization steps in recipe_Zhang17() already used around 70GB RAM - is this expected (the readme says around 30GB should be...

Hi, you can preprocess your data and pass it through all at once. Generally good to do pca (depends on what your features are though)

Hi! Thanks so much for reaching out. Let me check and get back to you in a couple of days. We are in the process of updating the tutorials to...

@revolvefire Hi, i've put up a simple scATAC-seq [tutorial](https://github.com/ShobiStassen/VIA/blob/master/Jupyter%20Notebooks/scATAC-seq_HumanHematopoiesis.ipynb) for you, hopefully it helps get you started

@A-legac45 Hi, generally speaking you would need to integrate your data and then run some for of dimensionality reduction (like PCA, typically 10-100PCs) before passing your features to StaVia

hi @A-legac45 , Im not too familiar with the details of a joint analysis for paired data where the cells are the anchor points (i.e. you have multimodal measurements for...

hi @A-legac45 you only need to provide a start state. the ends states are auto-predicted. the start state can be auto-predicted if you have RNA-velocity, but I would say that...