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pinellolab
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Hi, I have precomputed seurat objects. Can I use these objects? or any example?
I want to run about 50~ 200k cells trajectory. is there multicore or multithreading option?
I am trying to use a STREAM figure for publication and I did not see any option in the plot_stream function where the line size can be increased so it...
Hi, when I run the example for scRNA-seq: 1.1-STREAM_scRNA-seq (Bifurcation).ipynb. the program is fine, but there is no plot show in the screen or can't save as pdf files with...
Hello, After creating my plot stream, I am having trouble using detect_leaf_markers. There seems to be an issue with the keys, but I am not sure how to proceed. Here...
Hello! I am running the code used in the tutorial on my scRNA-seq data and everything was fine until I ran this line: st.plot_dimension_reduction(adata,color=['label','n_genes'],show_graph=False,show_text=False) It gives me the following error...
Hello, It seems that there is no se method for map_new_data in stream version 1 (whereas it was available in version 0.4). Is it normal? Thank you for the support.
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...
I am getting this error when I try to run it directly through python script any particular reason for this? `Traceback (most recent call last): File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 385, in...
Hi, How can I incorporate homer pwms motif list and mouse pwms v2 list into the STREAM_scATAC-seq-motif.ipynb? Thanks! SH
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STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data