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2
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84
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FilterByExpr low counts with small sample size
edgeR
22 hours ago • updated 18 minutes ago
Jonathan
▴ 10
1
vote
2
replies
51
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 hours ago • updated 39 minutes ago
Sherin
• 0
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 57 minutes ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
770
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
7 days ago • updated 1 hour ago
Chris
• 0
2
votes
3
replies
619
views
DESeq2 setting significant p-value
DESeq2
updated 2 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
1
reply
34
views
Input Question for deseq.r
RSeqAn
updated 3 hours ago by
ATpoint
★ 4.0k • written 21 hours ago by
Nina
• 0
0
votes
1
reply
56
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 3 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
3
replies
155
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 3 hours ago by
ATpoint
★ 4.0k • written 6 days ago by
schlumbohm
• 0
0
votes
0
replies
12
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
4 hours ago
Alessia
• 0
0
votes
0
replies
18
views
rlog transformation
DESeq2
5 hours ago
ishij9717
• 0
0
votes
2
replies
270
views
DESeq filtering specific to contrasts
DESeq2
updated 5 hours ago by
Carlin95
• 0 • written 8 weeks ago by
Emma
• 0
3
votes
3
replies
122
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
6 days ago • updated 6 hours ago
jacques.imbert
• 0
0
votes
0
replies
17
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
6 hours ago
09191919
• 0
0
votes
0
replies
28
views
Log-cpm values from limma
limma
edgeR
RNASeq
7 hours ago
Shaimaa Gamal
• 0
0
votes
0
replies
17
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 hours ago
Le
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 14 hours ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
4
votes
8
replies
280
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 15 hours ago by
Peter Hickey
▴ 740 • written 7 days ago by
Juan Higareda
• 0
0
votes
6
replies
139
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 16 hours ago by
Gordon Smyth
50k • written 1 day ago by
hortense96
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 21 hours ago
shepherl
3.8k
0
votes
2
replies
865
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 22 hours ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
0
votes
0
replies
30
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
1 day ago • updated 23 hours ago
ussarizona
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 1 day ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
0
votes
0
replies
26
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
1 day ago
lonn
• 0
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
0
votes
0
replies
25
views
News:
Services
flowBeads
1 day ago
creativepeptides2018
• 0
0
votes
0
replies
21
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Enzyme Engineering
BioTIP
1 day ago
bocchemistry
• 0
0
votes
0
replies
26
views
News:
TIDES USA 2024
flowBeads
1 day ago
bocsci11
• 0
0
votes
0
replies
44
views
covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
0
votes
0
replies
39
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
1 day ago
Maliha Tabassum
• 0
0
votes
3
replies
163
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
0
votes
0
replies
32
views
Adding columns to DEXSeqResults object
DEXSeq
1 day ago
Clyde
• 0
0
votes
4
replies
550
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 1 day ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
4
replies
107
views
flowStats Search Error
flowStats
updated 1 day ago by
shepherl
3.8k • written 2 days ago by
tholmes
• 0
0
votes
1
reply
82
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
tian.liu0720
• 0
1
vote
2
replies
68
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
2 days ago
Ana
• 0
0
votes
1
reply
62
views
what is the sampleFiles
chipseq
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
zhulin
• 0
0
votes
3
replies
132
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
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
0
votes
1
reply
98
views
Differentially expressed genes in monocle pseudotime
monocle
updated 2 days ago by
Gordon Smyth
50k • written 4 days ago by
kthapa
• 0
5
votes
12
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 days ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
2
replies
127
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 2 days ago
Henry
▴ 10
2
votes
3
replies
224
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
3 days ago • updated 2 days ago
daniel.carbajo
• 0
0
votes
1
reply
101
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 2 days ago by
kamryncole1963
• 0 • written 7 days ago by
Sara
• 0
0
votes
4
replies
2.6k
views
SingleR Label.Ont
SingleR
updated 2 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
0
replies
48
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
0
votes
0
replies
37
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
2 days ago
Henry
▴ 10
1
vote
2
replies
209
views
GSVA error
GSVA
4 days ago • updated 2 days ago
Alex
• 0
1
vote
1
reply
155
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 3 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
0
votes
1
reply
87
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
1
vote
3
replies
294
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 3 days ago by
Gordon Smyth
50k • written 8 days ago by
Simran
• 0
69 results • Page
1 of 2
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist
by
Sherin
• 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2
by
Elizabeth
• 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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