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0
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8
views
FDR via q-value
qvalue
16 minutes ago
John
• 0
0
votes
0
replies
12
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
2 hours ago
catv
• 0
0
votes
3
replies
40
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 2 hours ago by
James W. MacDonald
65k • written 4 hours ago by
bas_work
▴ 30
1
vote
0
replies
31
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
5 hours ago • updated 20 minutes ago
BioinfGuru
▴ 30
0
votes
2
replies
47
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
9 hours ago • updated 8 hours ago
prity6459
• 0
1
vote
2
replies
62
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 hours ago by
James W. MacDonald
65k • written 20 hours ago by
sansan
• 0
0
votes
4
replies
76
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
22 hours ago • updated 20 hours ago
sropri
• 0
0
votes
0
replies
24
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
23 hours ago
Mirella Aurora
• 0
0
votes
3
replies
71
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 7 hours ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
0
votes
0
replies
35
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
52
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
ishij9717
• 0
0
votes
1
reply
48
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
09191919
• 0
0
votes
1
reply
61
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
1
vote
2
replies
131
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 21 hours ago
Le
• 0
1
vote
2
replies
85
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago
Sherin
• 0
0
votes
1
reply
53
views
Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 1 day ago by
Nina
• 0
0
votes
4
replies
167
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 1 hour ago
Jonathan
▴ 10
0
votes
3
replies
107
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 10 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
1
reply
55
views
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
ussarizona
• 0
0
votes
1
reply
74
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
quanah.hudson
• 0
0
votes
6
replies
153
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
hortense96
• 0
0
votes
0
replies
37
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flowBeads
2 days ago
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0
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1
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73
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covariate with negative and positive values
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
1
reply
73
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
0
replies
48
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
2 days ago
Maliha Tabassum
• 0
1
vote
2
replies
79
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
3 days ago
Ana
• 0
0
votes
1
reply
71
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zhulin
• 0
0
votes
4
replies
117
views
flowStats Search Error
flowStats
updated 2 days ago by
shepherl
3.8k • written 3 days ago by
tholmes
• 0
0
votes
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
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SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
43
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 days ago
Henry
▴ 10
0
votes
3
replies
140
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
249
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago
daniel.carbajo
• 0
0
votes
4
replies
193
views
DEG with low counts
DESeq2
updated 6 hours ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
1
vote
2
replies
228
views
GSVA error
GSVA
5 days ago • updated 4 days ago
Alex
• 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
111
views
Differentially expressed genes in monocle pseudotime
monocle
updated 3 days ago by
Gordon Smyth
50k • written 5 days ago by
kthapa
• 0
0
votes
1
reply
93
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 3 days ago by
James W. MacDonald
65k • written 5 days ago by
tian.liu0720
• 0
2
votes
2
replies
135
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago
Henry
▴ 10
1
vote
2
replies
153
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
2
votes
2
replies
148
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
7 days ago • updated 6 days ago
julia_mcdonough
• 0
3
votes
3
replies
136
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
2
votes
2
replies
135
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago
daniel.carbajo
• 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
4
votes
8
replies
295
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 17 hours ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
0
votes
1
reply
107
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 3 days ago by
kamryncole1963
• 0 • written 8 days ago by
Sara
• 0
1
vote
1
reply
160
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 4 days ago by
Michael Love
41k • written 8 days ago by
Weiqian
▴ 10
5
votes
9
replies
798
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
Chris
• 0
77 results • Page
1 of 2
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
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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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