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MEDIP-seq
•
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0
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replies
696
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
21 months ago
Luomeng
• 0
7
votes
9
replies
2.0k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.5 years ago
rtrivedi1
▴ 10
4
votes
5
replies
1.5k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 3.2 years ago by
Lukas
▴ 20 • written 5.0 years ago by
lshepard
▴ 40
0
votes
0
replies
879
views
Calculating short read coverage at genome wide windows for create.set- MEDIPS
medip-seq
createset
updated 5.9 years ago by
Bioconductor Community
0 • written 6.0 years ago by
oussama.badad
• 0
1
vote
2
replies
1.1k
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 6.0 years ago by
Lukas Chavez
▴ 570 • written 6.0 years ago by
mtefit
• 0
0
votes
0
replies
946
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
6.0 years ago
saripalligautam86
▴ 10
1
vote
6
replies
2.2k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.7 years ago by
Lukas Chavez
▴ 570 • written 6.7 years ago by
vjain
• 0
16
votes
12
replies
7.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 11 weeks ago by
khanwaled68
• 0 • written 8.7 years ago by
florian.noack
▴ 60
0
votes
6
replies
2.1k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
8.3 years ago • updated 7.4 years ago
stb
• 0
3
votes
5
replies
1.9k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 7.5 years ago by
Matthias Lienhard
▴ 280 • written 7.5 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.4k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 7.5 years ago by
Lukas Chavez
▴ 570 • written 7.5 years ago by
anupriyaverma1408
• 0
0
votes
1
reply
1.3k
views
Insertion size when using 'paired' in MEDIPS.createSet()
medips
R
medip-seq
pair-end reads
updated 8.0 years ago by
Lukas Chavez
▴ 570 • written 8.0 years ago by
stb
• 0
0
votes
1
reply
1.2k
views
How does the 'paired' argument works in MeDIPS 1.23.2
medips
medip-seq
R
pair-end reads
updated 8.2 years ago by
Lukas Chavez
▴ 570 • written 8.2 years ago by
stb
• 0
1
vote
1
reply
1.7k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 8.3 years ago by
Lukas Chavez
▴ 570 • written 8.3 years ago by
stb
• 0
0
votes
0
replies
1.5k
views
count overlapping reads for CpG islands and annotate with gene names?
annotation
chippeakanno
rattus norvegicus
medip-seq
8.7 years ago
Vang Le
▴ 80
15 results • Page
1 of 1
Recent ...
Replies
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
You will probably have to ask the Signac people. I don't know exactly what is going on under the hood for `AddMotif`, but the `EnsDb` seems…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…
Comment: WGCNA with TPM tables
by
ATpoint
★ 4.5k
WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…
Votes
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
A: ANOVA-like test with edgeR
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