Bioconductor Mirna-seq

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deseq2 rnaseq mirna-seq differential gene expression

written 6.1 years ago by klalit1803 • 0

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mirna-seq limma

updated 5.6 years ago by Gordon Smyth 50k • written 5.6 years ago by Michael Stone • 0

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mirna-seq

updated 5.8 years ago by Levi Waldron ★ 1.1k • written 5.8 years ago by ndiayediop2 • 0

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mirna-seq

5.9 years ago • updated 5.8 years ago ndiayediop2 • 0

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r survival analysis rtcga tcgabiolinks mirna-seq

5.9 years ago atakanekiz ▴ 30

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686

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deseq2 differentially expression mirna-seq mirna target prediction

updated 5.9 years ago by Michael Love 41k • written 5.9 years ago by Björn • 0

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1000

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DESeq2 mirna-seq small RNA-seq

updated 6.3 years ago by Michael Love 41k • written 6.3 years ago by CandiceChuDVM ▴ 40

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deseq2 mirna-seq experimental design differential expression

updated 6.9 years ago by Gavin Kelly ▴ 680 • written 6.9 years ago by francesco.gandolfi ▴ 10

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miRNA mirna-seq

updated 7.1 years ago by Jon Bråte ▴ 250 • written 7.1 years ago by just • 0

9 results • Page 1 of 1

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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0

Understood, Thank you very much for the reply, very kind.

Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k

"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k

These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…

Comment: DEG with low counts by Michael Love 41k

These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…

Comment: DESeq filtering specific to contrasts by Michael Love 41k

If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…

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Install/Switch between multiple versions of R, Rstudio, and Bioconductor

A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

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