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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
just now
prity6459
• 0
0
votes
0
replies
14
views
Peptide Conjugated Nanoparticles
BiocHubsShiny
4 hours ago
beikrystal25
• 0
1
vote
1
reply
41
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 10 hours ago by
Guido Hooiveld
★ 3.9k • written 10 hours ago by
sansan
• 0
0
votes
4
replies
65
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
13 hours ago • updated 11 hours ago
sropri
• 0
0
votes
0
replies
19
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
14 hours ago
Mirella Aurora
• 0
0
votes
0
replies
26
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
14 hours ago
prity6459
• 0
0
votes
1
reply
38
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 16 hours ago by
Alejandro Reyes
★ 1.9k • written 20 hours ago by
Alessia
• 0
0
votes
1
reply
62
views
Adding columns to DEXSeqResults object
DEXSeq
updated 16 hours ago by
Alejandro Reyes
★ 1.9k • written 2 days ago by
Clyde
• 0
0
votes
0
replies
24
views
Warning while loading DEP package
DEP
updated 16 hours ago by
shepherl
3.8k • written 16 hours ago by
Namrata
• 0
0
votes
1
reply
42
views
rlog transformation
DESeq2
updated 16 hours ago by
Michael Love
41k • written 22 hours ago by
ishij9717
• 0
0
votes
1
reply
39
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 16 hours ago by
Michael Love
41k • written 22 hours ago by
09191919
• 0
0
votes
1
reply
51
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 16 hours ago by
Michael Love
41k • written 1 day ago by
ussarizona
• 0
0
votes
1
reply
70
views
covariate with negative and positive values
DESeq2
updated 16 hours ago by
Michael Love
41k • written 2 days ago by
Brynn
• 0
0
votes
1
reply
70
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
quanah.hudson
• 0
0
votes
0
replies
36
views
Log-cpm values from limma
limma
edgeR
RNASeq
1 day ago
Shaimaa Gamal
• 0
1
vote
2
replies
116
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 12 hours ago
Le
• 0
1
vote
2
replies
78
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago • updated 17 hours ago
Sherin
• 0
0
votes
1
reply
49
views
Input Question for deseq.r
RSeqAn
updated 20 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
Nina
• 0
0
votes
2
replies
114
views
FilterByExpr low counts with small sample size
edgeR
1 day ago • updated 15 hours ago
Jonathan
▴ 10
0
votes
3
replies
71
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 41 minutes ago by
ATpoint
★ 4.0k • written 1 day ago by
lonn
• 0
0
votes
6
replies
148
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
hortense96
• 0
0
votes
0
replies
33
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News:
Services
flowBeads
1 day ago
creativepeptides2018
• 0
0
votes
0
replies
27
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Enzyme Engineering
BioTIP
1 day ago
bocchemistry
• 0
0
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0
replies
33
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News:
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flowBeads
2 days ago
bocsci11
• 0
0
votes
0
replies
44
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
2 days ago
Maliha Tabassum
• 0
0
votes
4
replies
115
views
flowStats Search Error
flowStats
updated 2 days ago by
shepherl
3.8k • written 3 days ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 1 day ago
shepherl
3.8k
0
votes
1
reply
92
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
tian.liu0720
• 0
1
vote
2
replies
76
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
2 days ago
Ana
• 0
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
70
views
what is the sampleFiles
chipseq
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
zhulin
• 0
0
votes
1
reply
107
views
Differentially expressed genes in monocle pseudotime
monocle
updated 2 days ago by
Gordon Smyth
50k • written 5 days ago by
kthapa
• 0
4
votes
8
replies
291
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 8 hours ago by
Peter Hickey
▴ 740 • written 7 days ago by
Juan Higareda
• 0
3
votes
3
replies
135
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
6 days ago • updated 22 hours ago
jacques.imbert
• 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 7 days ago by
Sara
• 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
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
43
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 days ago
Henry
▴ 10
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
0
votes
3
replies
173
views
DEG with low counts
DESeq2
4 days ago • updated 2 days ago
Rajat
• 0
1
vote
2
replies
223
views
GSVA error
GSVA
4 days ago • updated 3 days ago
Alex
• 0
2
votes
3
replies
242
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
257
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
1
vote
3
replies
302
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 3 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
0
votes
1
reply
667
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
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
6
replies
544
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 6 days ago
shepherl
3.8k
2
votes
2
replies
148
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
6 days ago
julia_mcdonough
• 0
2
votes
2
replies
133
views
[DiffBind] Obtaining normalization factors
DiffBind
6 days ago • updated 2 days ago
Henry
▴ 10
45,547 results • Page
1 of 911
Recent ...
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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Votes
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
Comment: Error in champ.load(): The following specified files do not exist
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