stereoscope

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Hi ! I installed stereoscope and I am trying to run it however I am facing lots of issues... One of the errors I get is the following : `Traceback...

ineskrd

Stereoscope is awesome! Just, could you please kindly tell us, when preparing for Spatial Transcriptomics (ST) Count Data File, how we can calculate for the first column? For example, for...

kevin-de-granta

Thank you for the code！ During the stereoscope test process, an error occurred. The error is as follows.  > TypeError: 'type' object is not subscriptable I don't know which...

DINGQIA

Hi, I wonder how to choose a better "batch size" for scRNA and ST data? Is it related to the number of "orig.ident"? Besides, it seems that in the tutoriol...

yunbokai

How can I get the top genes for a celltype?

2

Hello Alma!! :) Hope everything is going great! I have a quick question regarding some of the outputs of stereoscope. I am interested in looking at the genes that stereoscope...

jemorlanes

stereoscope test Error

2

Hi, I use `python -c "import stsc; print(stsc.__version__)"` and get the version 0.3.1.However, When i use the code `stereoscope test`, the Error is  `(stereoscope) D:\stereoscope\stereoscope>python -c "import stsc; print(stsc.__version__)"...

yunbokai

Hi there, When I run the code `stereoscope run --sc_cnt ../data/curated/*cnt*.tsv --sc_labels ../data/curated/*mta*.tsv -sce 75000 -o hippo_1 -n 5000 --st_cnt ../data/curated/st-hippo*tsv -ste 75000 --gpu -stb 100 -scb 100` I got...

yunbokai

Hello All, Thanks for the steroscope cool method!!! It lloks pretty good for my data. I need some help to plot all my celltype in the spatial data and get...

AkilaRanjith

running the stereoscope command for method comparison is throwing some error

10

foo@bar:~$ stereoscope run --sc_cnt synthetic/valid*cnt* --sc_labels synthetic/valid*mta* -scb 256 \ -sce 50000 --st_cnt synthetic/counts.st-hippo-comp.tsv -ste 50000 -o ../res/comp-stereoscope \ --gpu -lr 0.1 [2022-06-14 14:42:10,006 - stsc - INFO ] >>...

Shrabanti87

Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

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