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224
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fgsea significant result
fgsea
13 days ago • updated 12 days ago
Chris
▴ 10
0
votes
3
replies
222
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by
Michael Love
42k • written 12 days ago by
fduguchunhui
• 0
0
votes
4
replies
218
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
29 days ago
sropri
• 0
2
votes
2
replies
213
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
sansan
• 0
1
vote
2
replies
212
views
Improving the design matrices vignette in RNAseq123
RNAseq123
26 days ago • updated 12 days ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
211
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 29 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
0
votes
2
replies
209
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago
kcarey
• 0
2
votes
5
replies
208
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
2 days ago • updated 1 day ago
Patadù
▴ 10
1
vote
2
replies
203
views
Citation for edgeR user guide
edgeR
written 24 days ago by
k___
▴ 30
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 25 days ago by
taur.vil
• 0
0
votes
3
replies
188
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
24 days ago • updated 23 days ago
ATpoint
★ 4.1k
0
votes
3
replies
174
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
bas_work
▴ 30
0
votes
1
reply
173
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
0
votes
2
replies
168
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
18 days ago • updated 15 days ago
Aurora
• 0
2
votes
1
reply
168
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
e1271094
• 0
0
votes
3
replies
168
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 4 days ago
e1271094
• 0
0
votes
1
reply
166
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
1
reply
162
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
2
replies
161
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
3
replies
158
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 1 hour ago by
Michael Love
42k • written 1 day ago by
Ken C
• 0
0
votes
1
reply
158
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
1
vote
1
reply
156
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
marcusn
• 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
c53aba27
• 0
1
vote
1
reply
153
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 22 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 12 days ago by
Michael Love
42k • written 12 days ago by
Sara
• 0
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
29 days ago
prity6459
• 0
0
votes
0
replies
142
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
23 days ago • updated 15 days ago
glaciya2018
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 days ago by
Michael Love
42k • written 12 days ago by
mat149
▴ 70
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 26 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
0
votes
0
replies
136
views
Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago
Chris
▴ 10
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
4
votes
0
replies
135
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
16 days ago
shepherl
3.9k
0
votes
1
reply
132
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 16 days ago by
4r-rtg
• 0
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
126
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 5 days ago by
Guido Hooiveld
★ 4.0k • written 5 days ago by
aogunbaw
• 0
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
4
replies
123
views
error running enricher from clusterprofiler
clusterProfiler
cluster
3 days ago • updated 2 days ago
Yael
• 0
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 18 days ago by
shepherl
3.9k • written 18 days ago by
bounlu
• 0
0
votes
2
replies
122
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 6 days ago by
Seungmin
• 0
1
vote
2
replies
120
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago
Daniel
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago
Henry
▴ 10
2
votes
3
replies
115
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Guillermo
• 0
186 results • Page
3 of 4
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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