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MeDIP-seq
•
reset
0
votes
0
replies
517
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
14 months ago
Luomeng
• 0
7
votes
9
replies
1.6k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
2.9 years ago
rtrivedi1
▴ 10
4
votes
5
replies
1.3k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 2.6 years ago by
Lukas
▴ 20 • written 4.4 years ago by
lshepard
▴ 40
0
votes
0
replies
758
views
Calculating short read coverage at genome wide windows for create.set- MEDIPS
medip-seq
createset
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
oussama.badad
• 0
1
vote
2
replies
955
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.4 years ago by
Lukas Chavez
▴ 570 • written 5.4 years ago by
mtefit
• 0
0
votes
0
replies
807
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
5.4 years ago
saripalligautam86
▴ 10
1
vote
6
replies
1.9k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.1 years ago by
Lukas Chavez
▴ 570 • written 6.1 years ago by
vjain
• 0
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.1k • written 8.1 years ago by
florian.noack
▴ 60
0
votes
6
replies
1.9k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
7.7 years ago • updated 6.8 years ago
stb
• 0
3
votes
5
replies
1.6k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 6.9 years ago by
Matthias Lienhard
▴ 240 • written 6.9 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.2k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 6.9 years ago by
Lukas Chavez
▴ 570 • written 6.9 years ago by
anupriyaverma1408
• 0
0
votes
1
reply
1.1k
views
Insertion size when using 'paired' in MEDIPS.createSet()
medips
R
medip-seq
pair-end reads
updated 7.4 years ago by
Lukas Chavez
▴ 570 • written 7.4 years ago by
stb
• 0
0
votes
1
reply
1.1k
views
How does the 'paired' argument works in MeDIPS 1.23.2
medips
medip-seq
R
pair-end reads
updated 7.6 years ago by
Lukas Chavez
▴ 570 • written 7.6 years ago by
stb
• 0
1
vote
1
reply
1.5k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 7.7 years ago by
Lukas Chavez
▴ 570 • written 7.7 years ago by
stb
• 0
0
votes
0
replies
1.3k
views
count overlapping reads for CpG islands and annotate with gene names?
annotation
chippeakanno
rattus norvegicus
medip-seq
8.2 years ago
Vang Le
▴ 80
15 results • Page
1 of 1
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Replies
Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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