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839

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DESeq2 p-adjusted-value Logfoldchange

updated 2.3 years ago by Michael Love 41k • written 2.3 years ago by bjen731 ▴ 10

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7.1k

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deseq2 differential expression logfoldchange lfcshrink lfcthreshold

updated 2.9 years ago by Michael Love 41k • written 5.8 years ago by emi.sch ▴ 30

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deseq2 R logfoldchange rna-seq

4.9 years ago • updated 4.8 years ago pierre.marin • 0

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1.4k

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DESeq2 logfoldchange counts

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by A ▴ 40

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940

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noiseq logfoldchange

6.0 years ago Aurora ▴ 20

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1.1k

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deseq2 plotMA rnaseq logfoldchange

updated 6.1 years ago by Michael Love 41k • written 6.1 years ago by ap_vc21 • 0

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1.2k

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outliers deseq2 logfoldchange

6.3 years ago lirongrossmann ▴ 80

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1.5k

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deseq2 logfoldchange variancestabilizingtransformation

updated 6.5 years ago by Michael Love 41k • written 6.5 years ago by lirongrossmann ▴ 80

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2.8k

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deseq2 interactions logfoldchange

updated 6.7 years ago by Michael Love 41k • written 6.7 years ago by rrcutler ▴ 70

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1.8k

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deseq2 logfoldchange

updated 7.4 years ago by Michael Love 41k • written 7.4 years ago by rraadd_8 • 0

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1.1k

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limma logfoldchange

updated 7.7 years ago by Aaron Lun ★ 28k • written 7.7 years ago by szenitha ▴ 20

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1.2k

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limma logfoldchange

updated 7.8 years ago by Gordon Smyth 50k • written 7.8 years ago by moradzadeh_k921 • 0

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limma arrayweights logfoldchange neqc normalization

updated 7.9 years ago by svlachavas ▴ 830 • written 7.9 years ago by merella.stefania • 0

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1.8k

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deseq2 logfoldchange interactions

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by colaneri ▴ 30

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2.9k

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deseq2 logfoldchange

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by g.atla ▴ 10

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3.6k

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clustering pca deseq2 edger logfoldchange

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by g.atla ▴ 10

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dexseq logfoldchange exon usage

8.4 years ago Assa Yeroslaviz ★ 1.5k

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limma logfoldchange limma design matrix paired samples affymetrix microarrays

updated 8.6 years ago by Ryan C. Thompson ★ 7.9k • written 8.6 years ago by svlachavas ▴ 830

18 results • Page 1 of 1

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Answer: OrgDb for maize by James W. MacDonald 65k

``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…

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…

Votes

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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