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Showing :
no replicates
•
reset
0
votes
0
replies
708
views
MethylSig is not giving DMRs with no replicates
methylsig
no replicates
dmr
5.8 years ago
nilaycan
• 0
1
vote
5
replies
3.0k
views
steps to get up and down regulated genes using DESeq2
deseq2
without replicate
no replicates
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
Tony
• 0
4
votes
9
replies
10k
views
DESeq2, no replicate
deseq2
no replicates
high p-adj values
updated 21 months ago by
Michael Love
41k • written 6.6 years ago by
Mahtetie
• 0
4
votes
8
replies
1.8k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
6.7 years ago
Stefany Solano
• 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic
estimate dispersion value
glm
no replicates
deseq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
hwick1
▴ 20
5
votes
7
replies
4.6k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
7.1 years ago
BioinfGuru
▴ 30
6 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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Rory Stark
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