Updating dependencies

[nkanrar]

Hi, thanks for making this great package. I've been experimenting with different pseudotime analysis packages, especially those that can integrate well with both Python and R (I'm using Scanpy for pre-processing and clustering my data, and probably doing differential gene expression analysis in R--all in the same Jupyter notebook). Stream is a great analysis package, but I run into problems when I try to 1. convert an AnnData object to an object usable by R and 2. actually use R code in my Jupyter notebook. Specifically, I am using conda for package management, and Stream's dependencies for rpy2 are outdated on conda: Stream specifies 2.9.4--which I think comes from the older version of rpy2 available on channel R on conda--while the newest rpy2 version is 3.3.2--on channel conda-forge on conda. This makes it difficult to even install other packages that are a great part of the AnnData workflow that Stream uses--i.e. anndata2ri https://github.com/theislab/anndata2ri#troubleshooting which cannot download because the rpy2 versions conflict. I know that there's a great number of issues with R package version availability with conda, so I'm not sure if this is an issue that can be solved on your side, but I would appreciate any insights!