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Hi ZijieJin,
I tried the docker using first on my local but since the base image is not defined and my system is Mac I got incompatibility error! I tried on our hpc, since npc uses singularity I ha…
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Hi! I have a huge 10X scRNA-seq mouse data (~60Gb BAM file | ~50K cells from 12 mice) that I am trying to run on cellSNP-lite. I compiled cellSNP-lite in an HPC environment and I am running it from th…
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When there are multiple tissue sections in a Xenium experiment, it is often impossible to have them lie exactly along the XY axis.
Current rectangular crop function results in inclusion of other b…
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When using the stDiff-sc/dataset1_seq_1670.h5ad and stDiff-sp/dataset1_spatial_246_preprocess.h5ad datasets downloaded from Zenodo for training, I encountered the following error:
```bash
ValueErr…
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Hi,
I am processing an scRNA-seq dataset containing 14 samples. For each sample, I performed the standard QC filtering based on nFeatures and mitochondrial gene percentage, followed by the identifi…
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Hi Salmon team
Are there plans afoot to support quantification of scRNA-seq data with unique molecular identifiers (UMIs)? UMIs are very commonly used in scRNA-seq data now, and correct quantificatio…
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Hello! Our project is currently focused on burst kinetics, and we found your pipeline can estimate kinetic parameters from nonallele-specific scRNA-seq data. We downloaded nnRNA and have successfully …
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http://iregulon.aertslab.org/
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To prepare scRNA-seq data for BAF analysis, xcltk is used. However, xcltk current does not support mm10 mouse scRNA-seq data at the baf_pre_phase.sh step, as it only permits usage of a Sanger-phasing …
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hello,
thanks for this great tool!
![image](https://github.com/MarioniLab/sagenet/assets/13601652/32e240d5-2545-4204-b1f6-a0e202cf720b)
I downloaded the big file sagenet_paper.tar.gz.
The orig…