pip install cellxgeneand got a weird error I don’t understand
This may happen, especially as we work out bugs in our installation process! Please create a new Github issue, explain what you did, and include all the error messages you saw. It’d also be super helpful if you call
pip freeze and include the full output alongside your issue.
If your dataset requires gigabytes of disk space, you may need to select an appropriate storage format in order to effectively utilize
cellxgene. Tips and tricks:
cellxgeneis optimized for columnar data access. For large datasets, format the expression matrix (
.X) as either a SciPy CSC sparse matrix or a dense Numpy array (whichever creates a smaller
h5adfile). If you are using
cellxgene prepare, include the
--sparseflag to ensure
.Xis formatted as a CSC sparse matrix (by default,
.Xwill be a dense matrix).
cellxgeneloads the dataset into memory, and start time is directly proportional to
h5adfile size and the speed of your file system. Expect that large (e.g., million cell) datasets will take minutes to load, even on relatively fast computers with a high performance local hard drive. Once loaded, exploring metadata should still be quick. If this start time is a problem, try the
--backedflag, which will attempt to lazily load data as needed (caveat: subsequent data access may be slower).
--disable-diffexpflag. For datasets that are extremely large, you may also find the
--backedflag improves your ability to explore them.
This is likely because you do not have node and npm installed, we recommend using nvm if you’re new to using these tools.