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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
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Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions.
First, I examined th…
Answer: Finding duplicated entries in GRangesList
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Kevin Blighe
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4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data
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Kevin Blighe
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4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed.
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Kevin Blighe
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4.0k
Hello Rui Tang,
The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot
by
Kevin Blighe
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4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
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