STREAM

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Hello, I would like to know if there is a difference between "branch" and "leaf branch" ? There seems to be a difference between the two terms because "leaf branch"...

bellenger-l

I used singularity to pull stream container, then I Run singularity shell to spawn a new shell within stream container and interact with it as though it were a small...

xiaowenchenjax

Map new data when using Seurat object

9

Hi, I have precomputed two seurat objects. After infering trajectory for one seurat object, I'd like to map cells from the other seurat object to the precomputed trajectory. However, there...

PeggySze

STREAM2

1

When we meet with STREAM2? I can find STREAM2-web in this pinellolab git.

wajm

stream import in conda env

4

Hi when I tried to install stream in a new conda env as suggested, I get the following error when importing the package. ``` --------------------------------------------------------------------------- LookupError Traceback (most recent call...

ajitjohnson

plot function: branch or leaf

2

Hey! Thanks again for the great tool! I am still stick with it. :-) I noticed that the trajectory looks slight different in terms of different functions (`st.plot_stream_sc vs st.plot_stream`)....

MingBit

Error with st.plot_stream()

1

Hi, Really like what I've been able to do with the software so far. Unfortunately, the functionality I was most looking forward to using, the st.plot_stream() function, appears to be...

aradley

Hi all, I run the stream-web on docker at http://localhost:10001/. After I upload data it showed "Upload successful" and is keep showing loading. I open the windows powershell showed like...

Roger-GOAT

Plot Gene Expression

1

Love the tool! Is there some simple code for plotting the expression of a single gene on the subway plots or other plots as a heatmap? I can generate labels...

babramso

Too big memory needed in st.normalize

1

Hello, I test stream with the reference dataset (data_Nestorowa.tsv.gz) and follow the steps in the tutorial (https://nbviewer.jupyter.org/github/pinellolab/STREAM/blob/master/tutorial/1.2.use_vis.ipynb?flush_cache=true). However, the memory needs 100g at " st.normalize(adata,method='lib_size') ". Will this happen. thank...

liushang20