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DEseq2
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9
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12
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7.7k
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Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 20 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
13
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 minutes ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 1 day ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
636
views
DESeq2 setting significant p-value
DESeq2
updated 22 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
553
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 2 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
3
replies
278
views
DESeq filtering specific to contrasts
DESeq2
updated 11 minutes ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
179
views
DEG with low counts
DESeq2
updated 2 minutes ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 3 days ago by
Michael Love
41k • written 8 days ago by
Weiqian
▴ 10
1
vote
2
replies
152
views
Design Matrix within group comparison more than two groups
DESeq2
6 days ago • updated 5 days ago
hemantcnaik
• 0
0
votes
3
replies
138
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
109
views
Bioinformatics student
Des
DESeq2
updated 6 days ago by
hemantcnaik
• 0 • written 6 days ago by
Sahar
• 0
0
votes
3
replies
96
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 3 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
lonn
• 0
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
0
votes
1
reply
73
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 23 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
1
reply
71
views
covariate with negative and positive values
DESeq2
updated 19 hours ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
1
reply
53
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 19 hours ago by
Michael Love
41k • written 1 day ago by
ussarizona
• 0
0
votes
1
reply
46
views
rlog transformation
DESeq2
updated 19 hours ago by
Michael Love
41k • written 1 day ago by
ishij9717
• 0
0
votes
1
reply
44
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 19 hours ago by
Michael Love
41k • written 1 day ago by
09191919
• 0
18 results • Page
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Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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