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Hi,
I'm using version 1.96, and has the problem as following when running the PBMC tutorial:
>>> LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome,celltype,outdir,method…
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There appears to be protein coding sequences in RNAcentral. For example:
http://rnacentral.org/search?q=%22protein%22%20and%20not%20%22non-protein%22
http://rnacentral.org/search?q=hypothetical%20…
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For paired-ended RNA-seq, even it's much less than 200bp, do I still need to using the long-rna-seq-pipeline instead of the small-rna-seq-pipeline? Thanks.
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Hi! Impressive work!
I was wondering whether your package would support demultiplexing bulk RNA-seq? And nanopore-based (i.e. not Illumina short) reads? Is support for other genomes (e.g. other mam…
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Hi team,
Thank you very much for developing this amazing tool! Do you think Velocyto is suitable for analyzing single nucleus RNA-seq dataset as well? The reason why I ask this is because single nucl…
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#### Scientific goals
- Create correlation matrices for polyA samples and ribodeplete (stranded) samples using gene expression data.
- Generate gene outlier thresholds for ribodeplete samples.…
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Hi,
I was wondering whether RNA velocity works well for 5' 10x data and if the results are similar to 3' data?
Many thanks,
Lucy
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_From @olgabot on July 6, 2014 22:55_
Hi @jbenet and @maxogden! Thank you so much for the time you took to meet with @mlovci and me this weekend. Here's an overview of our current data management sit…
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From email chain with Rob:
```
Here’s a few stories based on [Treehouse’s](https://treehousegenomics.soe.ucsc.edu/) current Jupyter analysis [notebooks](https://github.com/UCSC-Treehouse/jupyterhub)…
kozbo updated
7 years ago
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Hi, I wonder if there is any function in celldancer which can generate the raw RNA velocity matrix. I intend to compare this method with other RNA velocity estimation method. Thanks a lot.