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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
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2
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689
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 15 months ago by • 0
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1.0k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 17 months ago by 43k • written 17 months ago by • 0
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539
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
20 months ago Virangika • 0
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DiffBind spike-in lib.sizes confusion
SpikeIn DiffBind
2.8 years ago • updated 2.7 years ago Weisheng • 0
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 19 months ago by • 0 • written 2.9 years ago by ▴ 10
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4
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3.1k
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.0 years ago • updated 2.9 years ago spg • 0
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.2 years ago Drew • 0
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1.1k
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Spike-In Cells for Normalization?
SpikeIn SingleCell
4.3 years ago mb1996 • 0
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2
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1.9k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.4 years ago • updated 4.3 years ago maria.soler • 0
7
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12
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 2.2 years ago by • 0 • written 4.8 years ago by • 0
1
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9
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4.8k
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 3.0 years ago by ▴ 670 • written 5.1 years ago by ▴ 10
13 results • Page 1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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