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What do you recommend to try out for "big data" but for RNA seq instead of single cell?
mdanb updated
2 years ago
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Hello!
I've been having issues adapting bulk rna seq data into cellchats pipeline. I want to compare the bulk rna sequencing reads of three purified celltypes with one purified celltype, and find w…
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Hi team,
In the Redeconve manual.ipynb, I noticed that you mentioned Redeconve can also be used for bulk RNA-seq deconvolution. Does this mean we can use scRNA as reference to deconvolute bulk RNA …
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The @PavlidisLab/curation team compiled a list of single-cell experiments that need special treatment on import. We can convert those into test cases.
## Bulk/single-cell mix
Contains a mixture …
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From my exposure to classic WGCNA and this package so far, it seems like classic WGCNA often assigns most genes to a module and leaves a very small grey module (especially when using filtered genes as…
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The MC2 Center data model does not currently enable assay-specific metadata to be recorded. Adding these models is a critical part of supporting data sharing and reuse. Potential models to add were or…
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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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I have a relatively large bulk RNA seq dataset (~ 1300 samples, from ~70 experiments) that I'd like to correct for significant batch effects. Is it valid/possible to apply BERMUDA to my dataset? Inste…
mdanb updated
3 years ago
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[Input data](https://galaxy.hyphy.org/u/stephenshank/h/drosophila-transcriptomics-training---input-data), [QC and mapping workflow](https://training.galaxyproject.org/training-material/topics/transcri…