Bioconductor Differential Analysis

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DiffBind PCA Differential Analysis

updated 5.2 years ago by Rory Stark ★ 5.2k • written 5.2 years ago by jrp208 • 0

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1.8k

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diffbind ATACseq ATAC counts differential analysis

updated 6.2 years ago by Rory Stark ★ 5.2k • written 6.2 years ago by pgontarz ▴ 10

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1.5k

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diffbind differential analysis genetics #chip-seq

updated 6.2 years ago by Rory Stark ★ 5.2k • written 6.2 years ago by ryclb22 • 0

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1.9k

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edgeR FDR p-value Benjamini-Hochberg Differential Analysis

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by ilovesuperheroes1993 • 0

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1.5k

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diffbind atac-seq differential analysis deseq2

updated 6.6 years ago by Rory Stark ★ 5.2k • written 6.6 years ago by duvaller • 0

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deseq2 deseq differential analysis proteomics

7.1 years ago blehtine • 0

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1.4k

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differential analysis differential gene expression coexpression correlation

updated 7.2 years ago by Peter Langfelder ★ 3.0k • written 7.2 years ago by hkarakurt ▴ 20

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2.7k

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mast single-cell rna-seq differential analysis

updated 6 weeks ago by achoppe ▴ 10 • written 7.4 years ago by shao ▴ 100

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1.4k

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reportingtools microarray annotation differential expression differential analysis

updated 7.4 years ago by James W. MacDonald 68k • written 7.4 years ago by jirkanov • 0

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5.2k

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deseq2 multiple factor design differential analysis differential gene expression

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by hsbio ▴ 10

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DiffBind dba.count Chip-Seq Differential analysis

updated 4.2 years ago by Goku • 0 • written 7.7 years ago by urjaswita ▴ 40

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Comment: Limma trend with limpa by Alejandro • 0

Dear Gordon, Thank you very much!

Answer: DESeq2 from phyloseq error by asafpr • 0

Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …

Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0

Thank you for your reply! There are some pretty big discrepancies in the total raw counts between samples: ![enter image description here…

Answer: Limma trend with limpa by Gordon Smyth 52k

Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …

Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

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Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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Popular Question to James W. MacDonald 68k