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Hi,
I got the following error when I ran multi_nichenet_analysis() on my dataset.
[1] "Calculate differential expression for all cell types"
[1] "DE analysis is done:"
[1] "included cell type…
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Unfortunately, due to annotation errors, our genes.tsv file sometimes contains more than one gene with the same name. If they both appear in the set of genes to be plotted by plot_expression_heatmap()…
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Hi,
Can the seurat v3 SCTransform module be used prior to harmony?
eg:
`pbmc_harmony_integrated % SCTransform(vars.to.regress = "percent.mt", return.only.var.genes =FALSE, verbose = TRUE) %>% RunP…
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I am attempting to use the mixedModelDE function for differential expression analysis (post- vs pre-treatment tissue) as per Section 7.3 in the GeoMx Workflows vignette (https://bioconductor.org/packa…
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conflicting-nd-annotations-new.xlsx
- [ ] AB | 2113913685 | Q0VCR0 | ETFR1_BOVIN | GO:0008150 | P | SWIS | ECO:0000250 (ISS) | GO_REF:0000024 | GO:0022904 | respiratory electron transport chain
…
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The use of the Friday standup calls to cover a more nuanced question in greater depth was discussed at the most recent Relay meeting, and this is the first of those questions of the month. Please use…
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Dear professor
I want to know where i can find this file when i try this great STitch3D.
`genes_new = pd.read_csv("./genes_new.txt")` in this part "Run STitch3D on the human heart dataset"
than…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/bartongroup/fenr
Confirm the following by editing…
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Hello!
I'm interested in using carnival for some time series RNAseq and ATACseq data. I have differentially expressed genes from RNAseq as well as transcription factors I've obtained from motif ana…