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Hello!
I have some seqFISH data from Spatial Genomics generated by their 'genePS' system. I was wondering if anyone had some code to import this data into a SpatialExperiment S4 R/Bioconductor clas…
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Hi I am following the tutorial code, but got the following error. May I know how to solve it? Thanks!
My adata is the data in the tutorial:
adata = sq.datasets.seqfish()
sc.pp.filter_genes(adata…
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I was running this code and found "ground_truth = read.csv('~/ST/CellGridDivide3/Out_cell_ratio_1x.csv',row.names=1)" in ./evaluation & visualization/seqFISH+_visualize.R. While I did not find "Out_ce…
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## Description
When I use `sq.pl.ligrec` after `sq.gr.ligrec(
adata,
n_perms=100,
cluster_key="cluster",
clusters=["Polydendrocytes", "Oligodendrocytes"],
)
`, it always …
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Context:
Downloaded and installed giotto last week of May and attempted to work through https://rubd.github.io/Giotto_site/articles/mini_seqfish.html. Made it successfully (most of way), but ja…
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I have considered a way to compute a gene expression correlation coefficient in a spatial context and it was lucky for me to find this method (copulacci). Our lab reviewed the bioinformatics paper rec…
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An user should leverage parallelism on HPC clusters to run starfish and process volumetric data like seqFISH data (s3://spacetx.starfish.data.public/seqfish/).
I am wondering if it is possible roughl…
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The spatial test does not work under windows.
It results in the following error message
```
Error using readtable (line 223)
Unable to open file '~/seqFISH_Temporary_file/Table_channel1.txt'.
…
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Hi,
Thanks for the useful scripts. But while I was reading the code, I found this function `colocalizeBarcodeV2_markedup_NO_INTENSITY` not defined in any of the scripts.
https://github.com/CaiG…
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Hi,
I am trying Giotto by docker
```
$ docker pull delron01/giotto:latest
$ docker run --rm -p 8787:8787 -e PASSWORD=mypassword delron01/giotto:latest
```
I learn Giotto according to this tutor…