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Rank
Views
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1
vote
4
replies
184
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 13 hours ago
winwater0928
• 0
1
vote
5
replies
302
views
fgsea fork
fgsea
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
yimjohns
• 0
1
vote
4
replies
140
views
minfi::read.metharray.exp
minfiData
minfi
updated 2 days ago by
Basti
▴ 780 • written 4 days ago by
clacarion
• 0
1
vote
2
replies
171
views
Design Matrix within group comparison more than two groups
DESeq2
14 days ago • updated 13 days ago
hemantcnaik
• 0
1
vote
4
replies
417
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 21 days ago by
Gordon Smyth
50k • written 23 days ago by
jari.karppinen
• 0
1
vote
3
replies
83
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 7 hours ago by
Michael Love
41k • written 1 day ago by
JalapenoCornbread
• 0
1
vote
2
replies
221
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 7 days ago
Weiqian
▴ 10
1
vote
2
replies
126
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago • updated 8 days ago
Sherin
• 0
1
vote
1
reply
162
views
Differentially expressed genes in monocle pseudotime
monocle
updated 10 days ago by
Gordon Smyth
50k • written 12 days ago by
kthapa
• 0
1
vote
2
replies
407
views
GSVA error
GSVA
12 days ago • updated 11 days ago
Alex
• 0
1
vote
13
replies
282
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
5 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Hong Thu
• 0
1
vote
3
replies
118
views
Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
93
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
2 days ago • updated 1 day ago
ATpoint
★ 4.0k
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 21 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
1
vote
7
replies
128
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
1 day ago • updated 3 hours ago
pl23
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 9 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
2
replies
114
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
10 days ago
Ana
• 0
1
vote
3
replies
817
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 2 days ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
0
replies
208
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
7 days ago
BioinfGuru
▴ 30
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
24 days ago • updated 23 days ago
Layal
• 0
1
vote
3
replies
255
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 29 days ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
1
vote
2
replies
204
views
MethylKit read issue
methylKit
updated 21 days ago by
James W. MacDonald
65k • written 26 days ago by
CHEN
• 0
1
vote
1
reply
64
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
fernanda.backsouza
▴ 10
1
vote
6
replies
462
views
GSVA on separate healthy and disease datasets
GSVA
updated 16 days ago by
James W. MacDonald
65k • written 17 days ago by
Lucy
▴ 60
1
vote
2
replies
934
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 3 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
3
replies
326
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 11 days ago by
Gordon Smyth
50k • written 16 days ago by
Simran
• 0
1
vote
4
replies
158
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 4 days ago by
James W. MacDonald
65k • written 8 days ago by
Mirella Aurora
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 22 days ago by
Michael Love
41k • written 23 days ago by
RL
• 0
1
vote
1
reply
90
views
Citation for edgeR user guide
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
k___
▴ 30
1
vote
2
replies
184
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 days ago
Le
• 0
1
vote
2
replies
154
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 6 hours ago
ussarizona
▴ 10
1
vote
3
replies
229
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
Shaimaa Gamal
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 25 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
7
replies
390
views
DESeq filtering specific to contrasts
DESeq2
updated 7 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
0
replies
77
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
11 days ago
Virangika
• 0
0
votes
1
reply
144
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by
Michael Love
41k • written 28 days ago by
Mikushi
• 0
0
votes
0
replies
88
views
flowDensity on a flowset
flowDensity
21 days ago
fredrikwallberg
• 0
0
votes
1
reply
98
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Leyre
• 0
0
votes
2
replies
767
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 10 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
7 days ago
prity6459
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
09191919
• 0
0
votes
2
replies
902
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
1
reply
98
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
taur.vil
• 0
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
23 days ago
Marianna
▴ 20
0
votes
2
replies
215
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
29 days ago • updated 24 days ago
w.cookson
• 0
0
votes
0
replies
79
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
22 days ago
Macsue
• 0
0
votes
5
replies
233
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
Gayatri
• 0
0
votes
0
replies
63
views
I am trying to detect alternative splicing.
ASpli
6 days ago
Sebashish
• 0
201 results • Page
2 of 5
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Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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