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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
0
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2
replies
411
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 5 months ago by • 0
0
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1
reply
589
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 7 months ago by 43k • written 7 months ago by • 0
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0
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328
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
10 months ago Virangika • 0
1
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2
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823
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DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
23 months ago Weisheng • 0
6
votes
2
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3.2k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by ▴ 10
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2
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2.3k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 9 months ago by • 0 • written 2.1 years ago by ▴ 10
3
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4
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2.4k
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.2 years ago • updated 2.1 years ago spg • 0
0
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0
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1.1k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.4 years ago Drew • 0
0
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0
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928
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Spike-In Cells for Normalization?
SpikeIn SingleCell
3.5 years ago mb1996 • 0
0
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2
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1.5k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.5 years ago maria.soler • 0
7
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12
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5.0k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 16 months ago by • 0 • written 4.0 years ago by • 0
1
vote
9
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3.9k
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 2.2 years ago by ▴ 670 • written 4.3 years ago by ▴ 10
13 results • Page 1 of 1
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Replies
Comment: GSVA on RNAseq data by Robert Castelo ★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell by James W. MacDonald 68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20 by James W. MacDonald 68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2 by caroline.zanchi • 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org by Sean Davis 21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
A: Rtracklayer fails to export TxDb as GFF3 without CDS
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