Bioconductor Volcanoplot

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943

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RNA-seq DESeq2 volcanoplot

updated 6 weeks ago by Michael Love 43k • written 6 weeks ago by nramakr ▴ 10

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637

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DESeq2 volcanoplot LRT

updated 4 months ago by Michael Love 43k • written 4 months ago by Eric • 0

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1.9k

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DESeq2 volcanoplot deseq HELP contrast

updated 22 months ago by Basti ▴ 780 • written 22 months ago by Michael • 0

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1.1k

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plot volcano volcanoplot

updated 22 months ago by Basti ▴ 780 • written 22 months ago by Sooni ▴ 10

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779

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limma DEGreport Volcanoplot

updated 24 months ago by Gordon Smyth 52k • written 24 months ago by Mohammad • 0

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2.6k

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EnhancedVolcano RNASeqR R volcanoplot

updated 4.1 years ago by Kevin Blighe ★ 4.0k • written 4.2 years ago by camillab. ▴ 10

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3.0k

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limma volcanoplot pvalue logFC

updated 5.8 years ago by Gordon Smyth 52k • written 5.8 years ago by xingxd16 ▴ 20

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7.4k

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limma microarray volcanoplot color

updated 6.2 years ago by Gordon Smyth 52k • written 6.2 years ago by dmm204 • 0

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7.8k

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volcanoplot

updated 7.1 years ago by thokall ▴ 160 • written 7.1 years ago by Nithisha ▴ 10

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1.3k

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diffbind chipseq volcanoplot ggplot2

updated 7.2 years ago by Rory Stark ★ 5.2k • written 7.2 years ago by rbronste ▴ 60

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2.0k

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volcanoplot design and contrast matrix

updated 7.2 years ago by Gordon Smyth 52k • written 7.2 years ago by marongiu.luigi • 0

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11k

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volcanoplot limma fdr

7.4 years ago • updated 4.1 years ago tcalvo ▴ 100

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7.5k

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limma volcanoplot

updated 7.4 years ago by Gordon Smyth 52k • written 10.2 years ago by mccallionc403 • 0

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1.4k

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limma volcanoplot

updated 8.6 years ago by Aaron Lun ★ 28k • written 8.6 years ago by mheydarpour ▴ 10

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6.1k

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limma plot.MA volcanoplot oligo

updated 9.5 years ago by Gordon Smyth 52k • written 9.5 years ago by Gabriel Nathan Kaufman, Mr ▴ 60

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3.4k

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cummerbund ggplot2 size r volcanoplot

updated 10.0 years ago by James W. MacDonald 67k • written 10.0 years ago by ianmisner17 ▴ 20

16 results • Page 1 of 1

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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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