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BiSeq
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0
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1
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1.0k
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Variogram-sill larger than 1, and negative p.li values in trimClusters-output
BiSeq
3.7 years ago
thomas.koefoed
• 0
0
votes
0
replies
1.1k
views
Does it make sense to use Biseq for DMPs/DMCs in addition to DMRs?
Biseq
Methylation
DMP
DMR
RRBS
5.2 years ago
i.s.castanho
• 0
0
votes
1
reply
1.4k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
5.3 years ago
akhaira
• 0
0
votes
1
reply
1.1k
views
testClusters and trimClusters error in BiSeq
BiSeq
testClusters
error
dmr
5.3 years ago
akhaira
• 0
2
votes
8
replies
1.6k
views
Reason for NA in table after beta regression?
biseq
beta regression
5.3 years ago
akhaira
• 0
0
votes
0
replies
719
views
What values to include for predictedMethNull in BiSeq
Biseq
5.3 years ago
akhaira
• 0
2
votes
10
replies
2.0k
views
How do you use the readBismark command in BiSeq properly?
BiSeq
DMR
updated 5.3 years ago by
James W. MacDonald
68k • written 5.4 years ago by
akhaira
• 0
1
vote
0
replies
905
views
Understanding ColData in BiSeq
BiSeq
Coldata
5.4 years ago
akhaira
• 0
0
votes
1
reply
988
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
5.4 years ago
AishaD
• 0
0
votes
1
reply
951
views
BiSeq - betaResults output only contains chr1 and chr2
biseq
betaRegression
RRBS
Methylation
5.6 years ago
i.s.castanho
• 0
0
votes
0
replies
1.1k
views
Beta Regression model with wald test - BiSeq - which test is used?
BiSeq
Wald test
Beta regression
6.7 years ago
mira
• 0
0
votes
1
reply
1.3k
views
Biseq installation error
biseq
package installation
r
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
lwh863
• 0
0
votes
0
replies
1.2k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq
ccle
7.2 years ago
spr
▴ 10
0
votes
1
reply
1.4k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 7.8 years ago by
Gordon Smyth
53k • written 7.8 years ago by
ahmad.moousavi
• 0
0
votes
1
reply
1.4k
views
BiSeq - modelling options betaRegression
biseq
RRBS
betaregression
8.6 years ago
l.eijssen
• 0
0
votes
3
replies
1.7k
views
BiSeq. Model beta regression on resampled data.
biseq
methylation
dmr analysis
updated 8.8 years ago by
Katja Hebestreit
▴ 130 • written 8.8 years ago by
jjalmagro
• 0
0
votes
6
replies
2.4k
views
BiSeq trimClusters error
biseq
error
trimClusters
updated 9.7 years ago by
Katja Hebestreit
▴ 130 • written 9.8 years ago by
kms68
• 0
1
vote
0
replies
2.0k
views
Multiple linear regression model for DMR detection?
methylation
linear model
dmr
bsseq
biseq
9.9 years ago
enricoferrero
▴ 680
4
votes
4
replies
2.3k
views
Unable to read data using readBismark in BiSeq
BiSeq
readBismark
updated 10.0 years ago by
James W. MacDonald
68k • written 10.0 years ago by
Neel Aluru
▴ 460
1
vote
2
replies
3.1k
views
BS-seq differential methylation analysis using continuous variable
dmr
methylation
deseq2
bsseq
biseq
updated 10.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 10.0 years ago by
enricoferrero
▴ 680
2
votes
15
replies
4.3k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
10.5 years ago • updated 10.4 years ago
mnaymik
▴ 10
0
votes
5
replies
2.6k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
10.5 years ago
maria.maqueda
• 0
0
votes
3
replies
2.1k
views
BiSeq - readBismark error
BiSeq
BiSeq
updated 11.7 years ago by
David Iles
▴ 130 • written 11.7 years ago by
Hans-Ulrich Klein
▴ 330
23 results • Page
1 of 1
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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…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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