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0
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0
replies
98
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
7 days ago
Eryn
• 0
0
votes
0
replies
65
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
7 days ago
Dennis
• 0
0
votes
1
reply
102
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
Lucie
• 0
8
votes
23
replies
724
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 6 days ago by
Robert Castelo
★ 3.2k • written 7 days ago by
Bine
▴ 40
0
votes
1
reply
102
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 7 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Merav
• 0
0
votes
2
replies
175
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
41k • written 12 days ago by
nhaus
▴ 30
0
votes
1
reply
120
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
Adelaide
• 0
0
votes
2
replies
209
views
Regressing out batch effects
DESeq2
updated 8 days ago by
Michael Love
41k • written 13 days ago by
kys91240
• 0
5
votes
6
replies
362
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 days ago by
ATpoint
★ 4.0k • written 8 days ago by
nhaus
▴ 30
0
votes
1
reply
115
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
zh9118
• 0
1
vote
6
replies
416
views
GSVA on separate healthy and disease datasets
GSVA
updated 7 days ago by
James W. MacDonald
65k • written 8 days ago by
Lucy
▴ 60
0
votes
0
replies
78
views
ggtree tip label position (depth)
ggtree
8 days ago • updated 7 days ago
Roope
• 0
2
votes
6
replies
301
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
9 days ago
Chris
• 0
0
votes
1
reply
142
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
BCS12
• 0
0
votes
0
replies
97
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
9 days ago
arne.sahm
• 0
0
votes
0
replies
70
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
9 days ago
Wolfgang Huber
★ 13k
1
vote
10
replies
373
views
Obtaining pheno data from CEL files
GEO
affy
15 days ago • updated 8 days ago
Kurtis
• 0
0
votes
1
reply
134
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 11 days ago by
Gordon Smyth
50k • written 12 days ago by
avery
• 0
1
vote
3
replies
212
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
184
views
MethylKit read issue
methylKit
updated 12 days ago by
James W. MacDonald
65k • written 17 days ago by
CHEN
• 0
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 12 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
0
votes
4
replies
270
views
Help with design.matrix
limma
12 days ago • updated 11 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
116
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
12 days ago
andromeda
• 0
0
votes
2
replies
127
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
153
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 12 days ago by
ATpoint
★ 4.0k • written 13 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
105
views
Granges regionCounts not returning the expected number of entries
methylKit
13 days ago • updated 12 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
74
views
flowDensity on a flowset
flowDensity
13 days ago
fredrikwallberg
• 0
1
vote
1
reply
143
views
DESeq2 - Missing values in count matrix
DESeq2
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Hong Thu
• 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 13 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
181
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 13 days ago by
Tim Peters
▴ 170 • written 14 days ago by
Kim
• 0
0
votes
0
replies
68
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
14 days ago
Macsue
• 0
1
vote
4
replies
397
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 14 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
724
views
error in install immunedeconv
Install
updated 14 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
388
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 14 days ago by
Michael Love
41k • written 14 days ago by
RL
• 0
0
votes
2
replies
160
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
14 days ago
Gimena
• 0
0
votes
2
replies
134
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
14 days ago
Marianna
▴ 20
2
votes
6
replies
1.2k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 15 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
279
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 7 days ago by
Tim Peters
▴ 170 • written 15 days ago by
s.malik
• 0
1
vote
1
reply
124
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
15 days ago • updated 14 days ago
Layal
• 0
0
votes
2
replies
200
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
20 days ago • updated 15 days ago
w.cookson
• 0
0
votes
2
replies
139
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
15 days ago • updated 14 days ago
michelafrancesconi8
• 0
0
votes
1
reply
105
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 15 days ago by
James W. MacDonald
65k • written 15 days ago by
Reeya
• 0
0
votes
4
replies
209
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
Aidan
• 0
0
votes
4
replies
377
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
16 days ago • updated 15 days ago
Lucy
▴ 60
0
votes
1
reply
89
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
Leyre
• 0
0
votes
2
replies
150
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
16 days ago • updated 15 days ago
Seongsu
• 0
0
votes
2
replies
153
views
Gene Ontology doubt
microbiomeExplorer
17 days ago • updated 13 days ago
Bhawna
• 0
0
votes
1
reply
145
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 16 days ago by
Michael Love
41k • written 19 days ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
125
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 15 days ago by
James W. MacDonald
65k • written 17 days ago by
ja569116
• 0
1,000 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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