cNMF
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dylkot
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Hi. While performing tutorial code, I got a problem. I installed cnmf followed by your instruction and performed "simulated data". But, when I did #6 line, I got an error...
Hello Dylan, I was wondering how you would adjust the convergence limit for the underlying NMF implementation from the `sklearn` package, so that the following warning goes away: ``` sklearn/decomposition/_nmf.py:1641:...
Good day, I am using cNMF in 10x scRNA data and run the whole pipeline without any problem, and the outputs look good except for the consensus matrix which is...
Hi! Sorry, I just want to make sure, the matrix that gets fed into the --tpm slot gets variance normalized?
Thank you for creating this excellent package! Following the provided tutorial (analyze_pbmc_example_data.ipynb), I successfully reproduced nearly all the results in my jupyter notebook, however, surprisingly, I found that the file...
Thanks for creating this great package! I ran into the same issue as the authors of issue #8, #10, #57 and #66, in which running the consensus step on the...
Hi, I encountered the "TypeError: H should have the same dtype as X. Got H.dtype = float64." when running the last step (`cnmf consensus`). I have tried all suggestions in...
I get a `ValueError` if the number of topics after density filtering is less than the number of desired components. ``` Traceback (most recent call last): File "/Users/scottgigante/envs/immunaISR/lib/python3.8/site-packages/cnmf/cnmf.py", line 727,...
`normalize_per_cell` raises `numpy.core._exceptions.UFuncTypeError` (see https://github.com/scverse/scanpy/issues/2500) and is deprecated.
Dear authors: Thank you for your work on developing the nice tool cNMF. When I run the PBMC tutorial [https://github.com/dylkot/cNMF/blob/master/Tutorials/analyze_pbmc_example_data.ipynb](url), I found that the gep_score ,the result matrix to select...
