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MeDIP-seq
•
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0
votes
0
replies
781
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
2.2 years ago
Luomeng
• 0
7
votes
9
replies
2.2k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
3.9 years ago
rtrivedi1
▴ 10
4
votes
5
replies
1.7k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 3.6 years ago by
Lukas
▴ 20 • written 5.4 years ago by
lshepard
▴ 40
0
votes
0
replies
944
views
Calculating short read coverage at genome wide windows for create.set- MEDIPS
medip-seq
createset
updated 6.3 years ago by
Bioconductor Community
0 • written 6.4 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 6.4 years ago by
Lukas Chavez
▴ 570 • written 6.4 years ago by
mtefit
• 0
0
votes
0
replies
1.0k
views
All fragments/sequences captured using MeDIP are methylated?
medip-seq
methylation
CpGs
6.5 years ago
saripalligautam86
▴ 10
1
vote
6
replies
2.4k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 7.1 years ago by
Lukas Chavez
▴ 570 • written 7.1 years ago by
vjain
• 0
16
votes
12
replies
8.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 7 months ago by
khanwaled68
• 0 • written 9.1 years ago by
florian.noack
▴ 60
0
votes
6
replies
2.3k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
8.7 years ago • updated 7.9 years ago
stb
• 0
3
votes
5
replies
2.0k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 8.0 years ago by
Matthias Lienhard
▴ 280 • written 8.0 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.5k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 8.0 years ago by
Lukas Chavez
▴ 570 • written 8.0 years ago by
anupriyaverma1408
• 0
0
votes
1
reply
1.4k
views
Insertion size when using 'paired' in MEDIPS.createSet()
medips
R
medip-seq
pair-end reads
updated 8.4 years ago by
Lukas Chavez
▴ 570 • written 8.4 years ago by
stb
• 0
0
votes
1
reply
1.3k
views
How does the 'paired' argument works in MeDIPS 1.23.2
medips
medip-seq
R
pair-end reads
updated 8.6 years ago by
Lukas Chavez
▴ 570 • written 8.6 years ago by
stb
• 0
1
vote
1
reply
1.8k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 8.7 years ago by
Lukas Chavez
▴ 570 • written 8.7 years ago by
stb
• 0
0
votes
0
replies
1.6k
views
count overlapping reads for CpG islands and annotate with gene names?
annotation
chippeakanno
rattus norvegicus
medip-seq
9.2 years ago
Vang Le
▴ 80
15 results • Page
1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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