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I am trying to use GSE124872 to annotate bulk RNA seq data but I'm having trouble creating an expression set from both of them. For GSE124872, there is no actually cell type in the metadata that is co…
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Hi,
great package. I was wondering if this form of batch integration is also applicable to bulk RNA-Seq data. Sure the data is less sparse, but would that be an issue?
Happy about any feedback…
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The title is the Q really - I have matched spatial transcriptomics data and bulk RNA-seq data and want to deconvolute the spatial data with the bulk data. Is this possible with cell2location or some o…
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Hello !
I am new to these kind of analyses and have been running ``oarfish`` (v.0.6.2) with the following parameters/options:
``--single-cell``, ``--alignments``, ``--model-coverage`` and ``--num…
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Hello,
I am working with bulk RNA seq data. I created a reference like shown below:
`kallisto index -i mouse_version111cdna Mus_musculus.GRCm39.cdna.all.fa.gz`
Then I created a t2g file using…
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For some reason, a very large portion of the values in the `p`, `padj`, and `lfc` arrays are NAs and I'm not sure why. I am using the raw counts for the bulk RNA-seq as input to CAR-seq.
Any help …
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Hello @masai1116,
Thank you again for sharing the code! I have some questions regarding RNA-seq reads.
In our test SHARE-seq data, if we filter R2 by polyT, `TTTTTT + 1 mismatch`, about 50% rea…
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Dear community and Alex,
I will be running alignment for bulk RNA.seq PDx samples (human + mouse). The basic concept that I could gather was, align to human and mouse, this will generate BAM files …
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Sub-task of #2
- [ ] 3a. CORTECON
- [ ] 3b. POU3F2 over-expression in neural progenitors (Pearl et al. in press)
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Hi
I am using raw count data from single cell RNA-seq and bulk RNA-seq.
I am currently stuck at running the deconvolution function solveDampenedWLS().
I get the error :
```
Error in solve…