Baysor

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Build CLI from source error

4

I am attempting to make the Baysor CLI from source without having Julia installed. I entered the commands on the front page of the repo ``` git clone https://github.com/kharchenkolab/Baysor.git cd...

pvtodorov

My code and process shown below root@c04e1c64b14a:~/sec# baysor run -s 150 -x x -y y --gene Gene cc.csv ┌ Warning: No config file provided. Using default parameters. └ @ Baysor...

Yingzzzzz

Updated Binary for Linux

5

I would like to try --no-ncv-estimation option to prevent Out of Memory errors. However, the only binary for linux available does not have this option. Could you please provide an...

arunchakra

Same issue as #18 though I have the -p option

3

Successfully ran things from the pciSeq example and still could not make the HTML files: ``` /home/segonzal/baysor run -i 500 -m 8 -s 14 -o ./output_no_dapi -p ./data/pciSeq_3-3.csv ``` Output:...

sebgoti

New to Julia over here, so this might be an easy problem to fix, but I was following the notebook from the introductory video and was not able to plot...

sebgoti

Installation Issue

4

Hi @VPetukhov When installing the Baysor by Building CLI application from source, I got the error: The manifest file you are using was most likely generated by a different version...

BoomStarcuc

Inconsistent cell number in the json file and cell stats file

2

Hi @VPetukhov I wonder how to plot the cells (in polygon shapes) in the 2D tissue dimension after I finished clustering and cell type annotation. I saw that the zoom-in...

zhanglab2008

Dear @VPetukhov , If I don't like the default color in the :ncv_color column of the df_spatial DataFrame, how can I change it to a customized color palette? I really...

zhanglab2008

Error estimating boundary polygons

5

I've gotten the same crash at the same point in processing twice which prevented the export of a GeoJSON file or cell shape plot. The run command and log output...

timwiggin

A question about prior segmentation

2

Hi @VPetukhov , I've got my cell segmentation plot after running `baysor run` with `[PRIOR_SEGMENTATION]` parameter and `prior-segmentation-confidence = 1` parameter. And my prior segmentation file is processed under your...

rocketeer1998