NameError: name 'analysis' 'np' 'plt' is not defined when running the MERFISH_POA.ipynb

[neugun]

Hi! Really nice tool. I found the ssam is really interesting and I am a new starter with the R. When I am trying to run the MERFISH_POA.ipynb within the Jupyter notebook, there throw me serval errors while I running it.

First, NameError: name 'analysis' 'np' and 'plt' are not defined and I attached a example error below.

NameError Traceback (most recent call last)
in
1 # this requires local R installation with packages 'sctransform' and 'feather'
----> 2 analysis.normalize_vectors_sctransform()
NameError: name 'analysis' is not defined

Second, this requires local R installation with packages 'sctransform' and 'feather'. I usually conda install r-packages. but It doesn't work at this time, maybe I didn't make a successful local R installation with packages 'sctransform' and 'feather'. Do you have any suggestions for installing these packages?

Thank you so much!
Best,
Wegood

[pjb7687]

Hi, I will update the requirements for the package. For conda installation of R packages I noticed that you also need to install openblas libraries with sctransform otherwise it throws error. I think the dependency is currently missing in the sctransform package.

[pjb7687]

In addition, conda package r-sctransform 0.3.1 seems to be broken. Would you also try installing 0.2.1 instead.