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MEDIP-seq
•
reset
0
votes
0
replies
526
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
761
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
959
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
810
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 6.9 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 7.0 years ago by
Lukas Chavez
▴ 570 • written 7.0 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
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: Adding a group of samples reduces DEGs in other groups
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
Answer: FilterByExpr low counts with small sample size
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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