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Dear Team,
I run Whippet on my paired-end, unstranded, polyA+ RNA-seq dataset. The dataset is of 75bp length (all reads in all samples have this length) and performed in triplicates per condition (…
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Compare transcriptomes of B-ALL cells from our RNA-seq to the transcriptomes from the paper:
`Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells…
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Hi all,
I am really interesting in using your R package to deconvulte some of my bulk RNA-seq data. I was just trying to use the example data which is loaded with the package but I have already encou…
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cc @ValWood @kimrutherford
What can we do nowadays to curate results from gene expression in a given mutant (over / under expressed transcripts)? A phaf file? I can imagine that certain genes will …
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Hi Tinyi,
Firstly, I would like to express my appreciation for developing BayesPrism, a user-friendly software that has significantly aided my research. However, I have encountered some issues duri…
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Hello, thank you for providing such a convenient method, I would like to know if the input bulk transcriptome data must be count? Can I use tpm as input?
thanks
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Hi your tutorial page mentioned that users could use other tools that yield transcriptomes as input to Swan; however, I saw that in the step of "Adding transcript models from a GTF", a gtf file ("all_…
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### Operating System
macOS
### Other Linux
_No response_
### Workflow Version
v1.1.1-g999fb4e
### Workflow Execution
Command line
### EPI2ME Version
_No response_
### CLI command run
./next…
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I am working on calling variants in spatial transcriptomics data (10x Visium). Since the sequencing depth of spatial transcriptome is poorer than single-cell data, I want to treat all reads in the bam…
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### Lung-specific gene expression
- Identify the expression pattern for the marker genes of tissue-resident T cells
- [ ] integrate chromatin profiles with expression to validate the utility of …
j3gu updated
10 months ago