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Hi,
I've loved using souporcell for my single nucleus RNAseq analysis. Thanks to Haynes and the team for making such a good program.
On one dataset, though, I saw a result in R* seurat analysis…
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Hello,
I would like to measure the average median intensity, is it possible to do this?
and another question is when I to mark the box in the "S" button:
- use filter on nuclei image…
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Hello,
First, thank you for creating this great documented pipeline.
Second, I have a few questions about the proccess of the data:
1. in the paper it was written that : "Fastq files were then use…
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Hello! I’m using alevin-fry to map and quantify single nuclei RNAseq data. I’m trying to merge technical replicates but need to use separate permit lists (each generated from a provided list of valid …
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If I analyze Single-nuclei RNA-seq (snRNA-seq) data, which parameter should I use?
I don't know `run10x` and `run_dropest` which one I should use.
Or velocyto can't analysis snRNA-seq data?
Thank…
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Before you fill all the informations here, please give a read at the guidelines:
https://github.com/gwen001/offsectools_www/issues/1
[link]https://github.com/AggressiveUser/AllForOne[/link]
[tags…
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We discussed this manuscript https://openreview.net/forum?id=S1gBgnR9Y7
Their setting is to use 1/3 of the images in the Cell Painting dataset that area also present in CHEMBL to predict 209 CHEMBL…
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When trying to normalize a dataframe, I noticed that pycytominer.normalize is acting on all the _Location_Center_X and Y columns (which are associated with objects' locations). The following code give…
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# Problem
When using the `chunk_size` parameter above 1000 with my code, it is causing the "ImageNumber" column in the per_nuclei.parquet file to start from 695 and not 1. This causes the file afte…
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Hello,
I am trying to import a multiframe tiff file in ilastik.
You only choose a single file. If your stack is contained in a single file (e.g. a multi-page tiff) please use the "Add File" butt…