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News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 20 minutes ago
shepherl
3.8k
0
votes
4
replies
164
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FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 1 hour ago
Jonathan
▴ 10
0
votes
7
replies
319
views
DESeq filtering specific to contrasts
DESeq2
updated 1 hour ago by
Michael Love
41k • written 9 weeks ago by
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• 0
5
votes
14
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views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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updated 1 hour ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
0
replies
12
views
RNAseq:Technical replicates from different batches
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BatchEffect
limma
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1 hour ago
catv
• 0
0
votes
2
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208
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
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18 days ago • updated 2 hours ago
isaac.vock
• 0
0
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3
replies
40
views
Error retrieving ensembl gene id using biomaRt...
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James W. MacDonald
65k • written 3 hours ago by
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▴ 30
2
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5
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656
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DESeq2 setting significant p-value
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updated 2 hours ago by
Michael Love
41k • written 5.0 years ago by
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▴ 10
1
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2
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62
views
OrgDb for maize
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biomaRt
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updated 4 hours ago by
James W. MacDonald
65k • written 19 hours ago by
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• 0
1
vote
0
replies
29
views
Tutorial:
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Install
4 hours ago
BioinfGuru
▴ 30
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 hours ago by
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• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
193
views
DEG with low counts
DESeq2
updated 5 hours ago by
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41k • written 4 days ago by
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• 0
6
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5
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375
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written 7 weeks ago by
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• 0
0
votes
3
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70
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Finding DEGs by using edgeR
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updated 7 hours ago by
Gordon Smyth
50k • written 23 hours ago by
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• 0
0
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2
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45
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
8 hours ago • updated 7 hours ago
prity6459
• 0
0
votes
1
reply
59
views
Log-cpm values from limma
limma
edgeR
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updated 8 hours ago by
Gordon Smyth
50k • written 1 day ago by
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• 0
0
votes
3
replies
107
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Differential peaks that were not identified in diffbind were identified in diseq2
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updated 9 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
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• 0
0
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2
replies
887
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Bioconductor
written 4.2 years ago by
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• 0
4
votes
8
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295
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Memory errors using read.bismark?
dmrseq
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updated 17 hours ago by
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11
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5
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Theoretical WGCNA Question
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Theory
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updated 19 hours ago by
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• 0 • written 9.1 years ago by
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▴ 150
0
votes
4
replies
75
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
22 hours ago • updated 20 hours ago
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• 0
1
vote
2
replies
131
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 21 hours ago
Le
• 0
1
vote
2
replies
750
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 21 hours ago by
sredemption
• 0 • written 13 months ago by
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▴ 10
0
votes
0
replies
23
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
23 hours ago
Mirella Aurora
• 0
0
votes
3
replies
190
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
0
votes
0
replies
34
views
Warning while loading DEP package
DEP
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
0
votes
1
reply
44
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 1 day ago by
Alessia
• 0
0
votes
1
reply
72
views
Adding columns to DEXSeqResults object
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Clyde
• 0
0
votes
1
reply
51
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
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• 0
0
votes
1
reply
48
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ONT long-read RNA sequencing - data analysis options
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updated 1 day ago by
Michael Love
41k • written 1 day ago by
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• 0
0
votes
1
reply
55
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
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• 0
0
votes
1
reply
73
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covariate with negative and positive values
DESeq2
updated 1 day ago by
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41k • written 2 days ago by
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1
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2
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ChAMP
1 day ago
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• 0
9
votes
12
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updated 1 day ago by
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• 0 • written 8.8 years ago by
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▴ 30
5
votes
9
replies
798
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Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
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• 0
0
votes
1
reply
52
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Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 1 day ago by
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• 0
0
votes
1
reply
74
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DESEQ2 output gives multiple groups when only 2 groups are present
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updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
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• 0
3
votes
3
replies
136
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Reading huge bismark coverage files using bbseq::read.bismark
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BiocGenerics
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Biobase
7 days ago • updated 1 day ago
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5
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9
replies
1.2k
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Batch correction and repeated measures
RUVSeq
sva
limma
updated 1 day ago by
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50k • written 6 months ago by
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▴ 10
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votes
6
replies
153
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Methylation Analysis experiment design using Limma
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limma
methylationArrayAnalysis
updated 1 day ago by
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50k • written 2 days ago by
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3
votes
18
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2.8k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
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2
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871
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 1 day ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
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7
replies
1.7k
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Error using champ.import
ChAMP
EPICv2
updated 2 days ago by
shilpa
• 0 • written 9 months ago by
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• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
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• 0 • written 10 months ago by
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0
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0
replies
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553
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How to correct for known and surrogate variables in DESeq2?
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limma
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202 results • Page
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Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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
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