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spikein
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Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Katerina
• 0
0
votes
2
replies
689
views
Analysis of transcription inhibition with DESeq2
SpikeIn
DESeq2
Normalization
written 15 months ago by
ADopico
• 0
0
votes
1
reply
1.0k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Ειρήνη
• 0
0
votes
0
replies
539
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
20 months ago
Virangika
• 0
1
vote
2
replies
1.1k
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
2.8 years ago • updated 2.7 years ago
Weisheng
• 0
6
votes
2
replies
4.2k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
kalavattam
▴ 10
0
votes
2
replies
2.9k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 19 months ago by
maria.soler
• 0 • written 2.9 years ago by
kalavattam
▴ 10
3
votes
4
replies
3.1k
views
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
0
votes
0
replies
1.4k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
4.2 years ago
Drew
• 0
0
votes
0
replies
1.1k
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
4.3 years ago
mb1996
• 0
0
votes
2
replies
1.9k
views
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
votes
12
replies
6.0k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 2.2 years ago by
Miguel
• 0 • written 4.8 years ago by
robert.chen
• 0
1
vote
9
replies
4.8k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 3.0 years ago by
Bogdan
▴ 670 • written 5.1 years ago by
Hesh
▴ 10
13 results • Page
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Replies
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
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