Bioconductor Salmon

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salmon edgeR tximport nf-core gene_counts

updated 16 days ago by i.atanasoai • 0 • written 15 months ago by mohammedtoufiq91 ▴ 10

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1.4k

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DESeq2 tximport counts Salmon

updated 10 weeks ago by Michael Love 41k • written 16 months ago by kiqbal • 0

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306

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swish salmon fishpond

updated 3 months ago by Michael Love 41k • written 3 months ago by Nicholas • 0

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2.8k

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salmon DESeq2

updated 5 months ago by bella.johnson.2022 • 0 • written 2.3 years ago by Sneha • 0

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429

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salmon tximport deseq2

updated 6 months ago by Michael Love 41k • written 6 months ago by Kayleigh • 0

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1.5k

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salmon IsoformSwitchAnalyzeR tximport RNASeqData

updated 9 months ago by k.vitting.seerup ▴ 120 • written 9 months ago by elva.gypsophila ▴ 10

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3.0k

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tximport dtu salmon TPM rnaseqDTU

written 5.1 years ago by fiona.dick91 ▴ 60

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687

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rna-seq salmon fishpond swish

updated 10 months ago by Michael Love 41k • written 10 months ago by samuelcjx • 0

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Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20

limma package also isn't available.Is there any information when these packages will be available?

Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0

Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k

Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…

Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k

For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…

Comment: fgsea significant result by Chris • 0

Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…

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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Handling multiple differential expression comparisons

Answer: fgsea significant result

package goseq seems to be not available on the latest version of R

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Scholar to ATpoint ★ 4.1k