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MeDIP-seq
•
reset
0
votes
0
replies
488
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
13 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
2.8 years ago
rtrivedi1
▴ 10
4
votes
5
replies
1.2k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 2.5 years ago by
Lukas
▴ 20 • written 4.3 years ago by
lshepard
▴ 40
0
votes
0
replies
743
views
Calculating short read coverage at genome wide windows for create.set- MEDIPS
medip-seq
createset
updated 5.2 years ago by
Bioconductor Community
0 • written 5.3 years ago by
oussama.badad
• 0
1
vote
2
replies
933
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.3 years ago by
Lukas Chavez
▴ 570 • written 5.3 years ago by
mtefit
• 0
0
votes
0
replies
790
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
5.3 years ago
saripalligautam86
▴ 10
1
vote
6
replies
1.8k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.0 years ago by
Lukas Chavez
▴ 570 • written 6.0 years ago by
vjain
• 0
16
votes
9
replies
6.3k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.4 years ago by
Rory Stark
★ 5.1k • written 8.0 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
7.6 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 6.8 years ago by
Matthias Lienhard
▴ 240 • written 6.8 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 7.3 years ago by
Lukas Chavez
▴ 570 • written 7.3 years ago by
stb
• 0
0
votes
1
reply
1.0k
views
How does the 'paired' argument works in MeDIPS 1.23.2
medips
medip-seq
R
pair-end reads
updated 7.5 years ago by
Lukas Chavez
▴ 570 • written 7.5 years ago by
stb
• 0
1
vote
1
reply
1.4k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 7.6 years ago by
Lukas Chavez
▴ 570 • written 7.6 years ago by
stb
• 0
0
votes
0
replies
1.2k
views
count overlapping reads for CpG islands and annotate with gene names?
annotation
chippeakanno
rattus norvegicus
medip-seq
8.1 years ago
Vang Le
▴ 80
15 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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