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Recent Replies
Answer: RNA-seq analysis
by
Gordon Smyth
★
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featureCounts is so fast that you simply try both strands on one of the BAM files. From R, just try:
```
library(Rsubread)
fc1 <- featureCo…
Answer: Liquid Biopsy datasets
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ehaag
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You could try the NIAID Data Ecosystem: https://data.niaid.nih.gov/
It's designed to help researchers find datasets from infectious and …
Answer: RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitne
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ehaag
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Check out the NIAID Data Ecosystem, which aggregates datasets related to RNA viruses including HIV, Influenza, and SARS-CoV-2: https://data…
Answer: Metagenomics mock datasets
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ehaag
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If you're still looking, the NIAID Data Ecosystem is a discovery portal for reusable datasets: https://data.niaid.nih.gov/
It integrates d…
Answer: RNA-seq analysis
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> require strand specific information
See the answers in --> https://www.biostars.org/p/9547560/ for tools that you can use with your alig…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
•
0
```
pheatmap(cent_expr_matrix, breaks = cent_expr_breaks,
cluster_rows=F,
cluster_cols=T,
cellwidth = 10,cellheight=8.6,
…
Answer: Using structure prediction approaches to predict interaction between two protein
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Mensur Dlakic
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> I am specifically looking for tools excelling without MSAs.
I don't think there is such a tool that will excel at predicting protein i…
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ATpoint
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ComBat-seq does not produce negative counts but preserves the integer nature. Thats the whole point of the method. Lets see your code and d…
Comment: Heatmap of a transformed deseq object with pheatmap
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Glad it helps you. You probably can remove the legend and color scale, or if you save the figure in PDF or SVG (I don't know whether SVG is…
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1769mkc
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Sorry for that, it is done by our moderator. I would keep that in mind
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The answer to this entirely depends on what you intend to do with the data you obtain. Without replicates, you will be able to make inferen…
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Based on some recent posts from OP this is (as long as it is the same data) for an aneuploid plant with polyploidy ranging widely from 8 to…
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I'm not experienced with this type of problem, but you may be able to get some coarse-level understanding of the plody by just looking at a…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
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Thank you very much ! Yes I guess I should center and scale. I am always uneasy about doing this, but this would make everything more reada…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
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I think you very very much for your help. It worked. I think I will have to take off the legend and add it separately though, because I am …
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