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Straight from live output. I used the weirdest genotype names I could get. Other than that, should be a standard wt vs mt analysis. It seems that the genotype names may be throwing some errors, but th…
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Looking at options for different formats:
[Previous version](https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/7-expression-analysis.html) of eel pond used RSEM, which basically allowed the use…
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Hi,
Thanks for making this tool available - most parts work on first attempt ;-)
However, the 'Expression Distribution' panel remains empty. Only horizontal gridlines and y-axis labels are visible…
kloot updated
1 month ago
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### Operating System
Windows 10
### Other Linux
Ubuntu
### Workflow Version
v24.04
### Workflow Execution
Command line
### EPI2ME Version
_No response_
### CLI command run
./nextflow run w…
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Hello,
I am trying to run a specific differential expression analysis on a 10X data set that I can't seem to get working. I have 4 samples that I have been assigned to 2 genotypes "WT" and "KO". Al…
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Requested by Eric. Pending some further information:
- What is the measurement type / technology type assay configuration to be used for this
- Specification for iRODS collection structure
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- [x] Gene set enrichment with `fgsea`.
- [ ] Phenotype prediction (with `phenopredict`?).
- [x] Differential expression with limma and proper design matrix.
- [x] Differential expression with DESe…
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Dear @Vivianstats ,
Could you kindly explain briefly how scLink can be used to perform differential co-expression analysis between case and control samples similar to what you performed using the brea…
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Hey Antonio
I'm starting a thread here like you suggested.
I wanted to use TCGAbiolink to study differential expression of miRNA across different cancer type. What I observe in the vignette is th…
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Dear cellxgene team,
first of all, thank you for developing and maintaining such a nice tool!
I am trying to analyze a citeseq dataset with cellxgene. The difference here is that instead of cells …