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spikein
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894
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Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Katerina
• 0
0
votes
2
replies
652
views
Analysis of transcription inhibition with DESeq2
SpikeIn
DESeq2
Normalization
written 14 months ago by
ADopico
• 0
0
votes
1
reply
924
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Ειρήνη
• 0
0
votes
0
replies
507
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 months ago
Virangika
• 0
1
vote
2
replies
992
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
2.6 years ago
Weisheng
• 0
6
votes
2
replies
4.1k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
kalavattam
▴ 10
0
votes
2
replies
2.8k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 17 months ago by
maria.soler
• 0 • written 2.7 years ago by
kalavattam
▴ 10
3
votes
4
replies
3.0k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
2.9 years ago • updated 2.8 years ago
spg
• 0
0
votes
0
replies
1.3k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
4.0 years ago
Drew
• 0
0
votes
0
replies
1.1k
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
4.2 years ago
mb1996
• 0
0
votes
2
replies
1.8k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
4.2 years ago
maria.soler
• 0
7
votes
12
replies
5.9k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 2.1 years ago by
Miguel
• 0 • written 4.6 years ago by
robert.chen
• 0
1
vote
9
replies
4.6k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 2.9 years ago by
Bogdan
▴ 670 • written 5.0 years ago by
Hesh
▴ 10
13 results • Page
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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