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3
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18
replies
2.8k
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News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 2 days ago
shepherl
3.8k
5
votes
14
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 1 day ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 5 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 6 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 1 day ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 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
4
votes
8
replies
297
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 19 hours ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 2 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
0
votes
7
replies
330
views
DESeq filtering specific to contrasts
DESeq2
updated 3 hours ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
5
votes
6
replies
380
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
0
votes
6
replies
552
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 2 hours ago
shepherl
3.8k
0
votes
6
replies
155
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
6
votes
5
replies
378
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
2
votes
5
replies
661
views
DESeq2 setting significant p-value
DESeq2
updated 5 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 21 hours ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
4
replies
194
views
DEG with low counts
DESeq2
updated 8 hours ago by
Michael Love
41k • written 4 days ago by
Rajat
• 0
0
votes
4
replies
169
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 3 hours ago
Jonathan
▴ 10
0
votes
4
replies
117
views
flowStats Search Error
flowStats
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
tholmes
• 0
0
votes
4
replies
554
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 3 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
4
replies
76
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago • updated 22 hours ago
sropri
• 0
0
votes
4
replies
2.8k
views
SingleR Label.Ont
SingleR
updated 3 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
3
replies
107
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 11 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
3
replies
43
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 hours ago by
James W. MacDonald
65k • written 5 hours ago by
bas_work
▴ 30
2
votes
3
replies
250
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
3
votes
3
replies
259
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
3
votes
3
replies
137
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 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
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
0
votes
3
replies
72
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 9 hours ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
1
vote
3
replies
304
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
2
votes
2
replies
135
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago
Henry
▴ 10
2
votes
2
replies
149
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
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
135
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago
daniel.carbajo
• 0
1
vote
2
replies
228
views
GSVA error
GSVA
5 days ago • updated 4 days ago
Alex
• 0
1
vote
2
replies
79
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
3 days ago
Ana
• 0
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 2 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
2
replies
85
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago
Sherin
• 0
1
vote
2
replies
750
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 23 hours ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
132
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 23 hours ago
Le
• 0
0
votes
2
replies
888
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
47
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
11 hours ago • updated 9 hours ago
prity6459
• 0
1
vote
2
replies
62
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 hours ago by
James W. MacDonald
65k • written 21 hours ago by
sansan
• 0
0
votes
2
replies
211
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 4 hours ago
isaac.vock
• 0
1
vote
2
replies
164
views
How to retrieve detailed regression results from deseq2
DESeq2
8 days ago • updated 23 minutes ago
Weiqian
▴ 10
0
votes
1
reply
74
views
Adding columns to DEXSeqResults object
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Clyde
• 0
0
votes
1
reply
74
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zhulin
• 0
77 results • Page
1 of 2
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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
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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