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1 vote
Accepted

module differential connectivity (MDC) analysis

Answer from @devon-ryan, converted from comments: They described how they did it in that paper, there's just not a tool for it. It's not part of anything. They describe the algorithm, maybe DGCA ...
0 votes

How can extract the list of genes name from the raw data in GEO?

Answer from @benn, converted from comments: You can find a step by step description in the limma user's guide. Just download the CEL files, and follow the user guide. [please edit to improve this ...
1 vote

Normalization of data with RPkM

It's very unlikely that "a RPKM analysis" is the right answer. Assuming you'd like to do differential expression, using tools like DESeq or EdgeR on the count table are likely to be a better ...
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1 vote

beginner RNA-seq Replicate papers

I like Gierlinksi, et al., Bioinformatics, 2015 for this type of problem. I like this paper because the methods are descriptive and clear, they have lots of figures that you can reproduce along the ...
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  • 1,142
0 votes

beginner RNA-seq Replicate papers

Here's https://drive.google.com/file/d/1Lwh6ofxi_bb92mB0HoRrMJObE1MmtcMi/view?usp=sharing It is from the book of Methods of mathematical oncology https://github.com/...
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0 votes

Grouping x-axis in scatter plot

You have two different types of values you want to display on the x-axis: Cluster (a categorical variable) and Count (a ...
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  • 1,142
1 vote
Accepted

Can I Incorporate svaseq() into GSEA/GSVA analysis?

Use removeBatchEffects from limma. The input counts should be on log scale, so vst and ...
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0 votes

Generate a single column from two different columns in the same format

I think this should be fairly straightforward: ...
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0 votes

Heatmap of motifs present in protein sequences

Firstly, the problem with your data is that it ain't aligned. Without that your motif positions are not relative from one protein to another. Basically you need to align it and there's no wriggle room....
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  • 7,284
0 votes

beginner RNA-seq Replicate papers

I am a beginner too. I will try the galaxy (training): https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
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2 votes
Accepted

how to calculate the expression values per gene for all cells

No Seurat function is needed. In the seurat object "cells", you can access the raw counts or normalized counts using cells@assays$RNA@counts (raw counts) ...
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  • 319
2 votes
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deseq2 full and reduced model interpretation

By fitting the full model ~FAB + Sex + Age + TMB + WBC + BM_percentage you can estimate the effect of FAB (or any of the other variables) on RNA expression after ...
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