Bioconductor BiocVersion

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BiocVersion OrgDb clusterProfiler

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docker BiocManager BiocVersion

updated 5.0 years ago by Martin Morgan 25k • written 5.0 years ago by Michael Steinbaugh ▴ 90

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BiocVersion

updated 2.7 years ago by shepherl 3.8k • written 2.7 years ago by J • 0

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versions BiocVersion dependencies

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BioCor bioc BiocVersion

5 months ago feifan • 0

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BiocVersion

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DESeq2 BiocVersion

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bioconductoroversight community BiocVersion news

updated 3.1 years ago by aedin • 0 • written 3.2 years ago by Matthew Ritchie ▴ 1000

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BiocVersion phangorn ShinyApps

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destiny BiocVersion

updated 2.8 years ago by shepherl 3.8k • written 2.8 years ago by Yiming ▴ 10

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massgeek Reactome Proteomics STRINGdb

3.4 years ago paula • 0

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bioconductoroversight news community BiocVersion

3.1 years ago Matthew Ritchie ▴ 1000

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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…

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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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