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medip-seq
•
reset
0
votes
0
replies
712
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
22 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
3.6 years ago
rtrivedi1
▴ 10
4
votes
5
replies
1.6k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 3.2 years ago by
Lukas
▴ 20 • written 5.1 years ago by
lshepard
▴ 40
0
votes
0
replies
888
views
Calculating short read coverage at genome wide windows for create.set- MEDIPS
medip-seq
createset
updated 6.0 years ago by
Bioconductor Community
0 • written 6.1 years ago by
oussama.badad
• 0
1
vote
2
replies
1.2k
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 6.1 years ago by
Lukas Chavez
▴ 570 • written 6.1 years ago by
mtefit
• 0
0
votes
0
replies
962
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
6.1 years ago
saripalligautam86
▴ 10
1
vote
6
replies
2.2k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.8 years ago by
Lukas Chavez
▴ 570 • written 6.8 years ago by
vjain
• 0
16
votes
12
replies
7.8k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 3 months ago by
khanwaled68
• 0 • written 8.8 years ago by
florian.noack
▴ 60
0
votes
6
replies
2.2k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
8.4 years ago • updated 7.5 years ago
stb
• 0
3
votes
5
replies
1.9k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 7.6 years ago by
Matthias Lienhard
▴ 280 • written 7.6 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.4k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 7.6 years ago by
Lukas Chavez
▴ 570 • written 7.6 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 8.1 years ago by
Lukas Chavez
▴ 570 • written 8.1 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 8.3 years ago by
Lukas Chavez
▴ 570 • written 8.3 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 8.4 years ago by
Lukas Chavez
▴ 570 • written 8.4 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
8.8 years ago
Vang Le
▴ 80
15 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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