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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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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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To support custom pre/post-processing, but also to allow composition of models, (together with @FynnBe and @constantinpape) we propose the follow workflow spec.
The idea is to define a list of ste…
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Hello,
I am doing single nuclei RNA seq and have issues with cellranger discarding lots of reads and would like to directly compare between optimizing the cellranger reference to deal with overlaps e…
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Hello - I have a scenario where I'd like to calculate orbitals and energy in a large system (let's say several molecules), then delete some molecules (both the nuclei and oribtals) and recalculate the…
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Hello,
I'm analysing single-cell full-length RNA sequencing data. I would like to perform an analysis on alternative splicing exons, which has been mentioned multiple times in your research group's…
weib3 updated
4 months ago
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Currently `cytominer_transport/_generator.py` combines objects based on "ImageNumber" and "ObjectNumber".
Instead, we should consider combining objects by their appropriate "Parent_{compartment}" a…
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It would be helpful for users
- [x] to fill ***Parent Objects*** (*Nuclei objects*, *Cells objects*, etc) where it 's possible when user adds *Main* modules.
- [x] to disable ***Run analysis*** …
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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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Project UUID: 9c20a245-f2c0-43ae-82c9-2232ec6b594f
Project Title: Transcriptomic classification of human retinal cell types with single-nuclei RNA-seq.
Project Short Name: snRNA-seq_for_human_retina…