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0
votes
0
replies
130
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
2
votes
6
replies
464
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
5 weeks ago
Chris
▴ 10
0
votes
1
reply
189
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
BCS12
• 0
0
votes
0
replies
175
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
5 weeks ago
arne.sahm
• 0
0
votes
0
replies
114
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
5 weeks ago
Wolfgang Huber
★ 13k
1
vote
10
replies
477
views
Obtaining pheno data from CEL files
GEO
affy
6 weeks ago • updated 5 weeks ago
Kurtis
• 0
0
votes
1
reply
187
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
avery
• 0
1
vote
3
replies
280
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
258
views
MethylKit read issue
methylKit
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
CHEN
• 0
1
vote
2
replies
3.2k
views
Extract genes from ggvenn?
ggvenn
updated 6 weeks ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
331
views
Help with design.matrix
limma
6 weeks ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
163
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
6 weeks ago
andromeda
• 0
0
votes
2
replies
183
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
joshua.mannheimer
• 0
2
votes
2
replies
219
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
145
views
Granges regionCounts not returning the expected number of entries
methylKit
6 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
117
views
flowDensity on a flowset
flowDensity
6 weeks ago
fredrikwallberg
• 0
1
vote
1
reply
189
views
DESeq2 - Missing values in count matrix
DESeq2
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Hong Thu
• 0
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 1 day ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
1
vote
2
replies
373
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 15 days ago
Kim
• 0
0
votes
0
replies
106
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
6 weeks ago
Macsue
• 0
1
vote
4
replies
463
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by
Amruta
• 0 • written 5.3 years ago by
r.tor
• 0
0
votes
2
replies
805
views
error in install immunedeconv
Install
updated 6 weeks ago by
Arash
• 0 • written 14 months ago by
fenglingao
• 0
1
vote
6
replies
459
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
RL
• 0
0
votes
2
replies
207
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 weeks ago
Gimena
• 0
0
votes
2
replies
197
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
6 weeks ago
Marianna
▴ 20
2
votes
6
replies
1.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 6 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
368
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 5 weeks ago by
Tim Peters
▴ 180 • written 6 weeks ago by
s.malik
• 0
1
vote
1
reply
173
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
6 weeks ago
Layal
• 0
0
votes
2
replies
242
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
7 weeks ago • updated 6 weeks ago
w.cookson
• 0
0
votes
2
replies
184
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
6 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
165
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Reeya
• 0
0
votes
4
replies
286
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
Aidan
• 0
0
votes
4
replies
448
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
6 weeks ago
Lucy
▴ 60
0
votes
1
reply
126
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Leyre
• 0
0
votes
2
replies
199
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
6 weeks ago
Seongsu
• 0
0
votes
2
replies
193
views
Gene Ontology doubt
microbiomeExplorer
6 weeks ago
Bhawna
• 0
0
votes
1
reply
193
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 6 weeks ago by
Michael Love
42k • written 7 weeks ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
176
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
ja569116
• 0
0
votes
2
replies
315
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
6 weeks ago
fer_talavera
• 0
0
votes
2
replies
283
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 29 days ago
isaac.vock
• 0
0
votes
7
replies
437
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
7 weeks ago • updated 6 weeks ago
needNGS
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago
Chris
▴ 10
3
votes
5
replies
413
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Fabian
• 0
0
votes
4
replies
264
views
Minfi - estimatecellscount
min
minfi
updated 19 days ago by
James W. MacDonald
65k • written 7 weeks ago by
clacarion
• 0
0
votes
0
replies
126
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 weeks ago
feather-W
• 0
0
votes
0
replies
123
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 weeks ago
Ankit
▴ 20
0
votes
6
replies
372
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Faisal
• 0
1
vote
5
replies
368
views
fgsea fork
fgsea
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
yimjohns
• 0
0
votes
1
reply
176
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 7 weeks ago by
Michael Love
42k • written 7 weeks ago by
Mikushi
• 0
45,668 results • Page
5 of 914
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
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: 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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