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Comment: FraserDataSet() error in FRASER
by
marco.barr
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170
Can you show the `colData` data? It’s important that `colData$sampleID` is identical to `rownames(colData)` and to the sample names in `jun…
Comment: Single cell expression and accessibility integration using cellxgene data
by
1769mkc
★
1.3k
thank you for the resources, will try and update
Answer: Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness
by
eric.blalock
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0
On the subject of DE, way back in the days of microarrays, this pooling/ sub-pooling issue was big. Gary Churchill warned everybody here
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Comment: Heatmap of a transformed deseq object with pheatmap
by
Mensur Dlakic
★
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When you save a plot in a vector format such as SVG or PDF, there will be objects that can be moved around as units. You can literally drag…
Comment: Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
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Charles-Alexandre Roy
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Here's the one-liner for Medhat's useful command:
```bash
head -n40 file.fastq | awk 'NR%4==0 {printf "%s", $0}' | od -A n -t u1 | awk 'BE…
Comment: Single cell expression and accessibility integration using cellxgene data
by
Bastien Hervé
6.2k
yes, you can try [this][1]
[1]: https://stuartlab.org/signac/reference/callpeaks
Comment: Single cell expression and accessibility integration using cellxgene data
by
1769mkc
★
1.3k
Naive question So that is the only information I would need for mac2 input?
Answer: Regressing variables for finding Differentially expressed genes
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What species are you working on and which cell types are you interesting in ?
As you don't have female disease samples it is complicated…
Comment: Single cell expression and accessibility integration using cellxgene data
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You can call peaks again from the fragments file using Macs2 like they did in the paper. Then you can add your `peaks x cells` matrix as a …
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It has nothing to do with readability but with transforming data to emphasize differences rather than absolute expression levels, see https…
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`p-value` and `FDR` are working in pairs.
Genes pvalue from null are expected to be distributed uniformly (even with pvalue < 0.05), so th…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
•
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I made I mistake I meant "the reference on the right, the group that was compared to it on the left".
I think you are right about the orde…
Comment: FraserDataSet() error in FRASER
by
n_navy
•
0
Thanks but still encounter the same problem;
> fds <- FraserDataSet(
workingDir = data_dir,
junctions = junctions,…
Comment: Reference-guided transcriptome assembly using multiple SRA experiments ?
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lieven.sterck
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Sounds like a sensible approach to me.
I'm sure that there must be papers around already that have done more or less the same, no? I'm th…
Comment: Heatmap of a transformed deseq object with pheatmap
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SamGG
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`rownames(expr_matrix) <- paste(genes,"-",gene_names)` will avoid to pass labels_row and allows to keep custom names synchronized with the …
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