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484
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queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
20 months ago
Dennis
• 0
0
votes
2
replies
2.8k
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 months ago by
Andrea
• 0 • written 20 months ago by
Lucie
• 0
8
votes
23
replies
6.0k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 20 months ago by
Robert Castelo
★ 3.4k • written 20 months ago by
Bine
▴ 50
0
votes
1
reply
997
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Merav
• 0
0
votes
2
replies
826
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 20 months ago by
Michael Love
43k • written 20 months ago by
nhaus
▴ 70
0
votes
1
reply
847
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Adelaide
• 0
0
votes
2
replies
768
views
Regressing out batch effects
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
kys91240
• 0
5
votes
6
replies
1.5k
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
nhaus
▴ 70
0
votes
1
reply
690
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
zh9118
• 0
1
vote
6
replies
1.5k
views
GSVA on separate healthy and disease datasets
GSVA
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Lucy
▴ 60
0
votes
0
replies
999
views
ggtree tip label position (depth)
ggtree
20 months ago
Roope
• 0
2
votes
6
replies
4.3k
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
20 months ago
Chris
▴ 20
0
votes
1
reply
617
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
BCS12
• 0
0
votes
0
replies
949
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
20 months ago
arne.sahm
• 0
0
votes
0
replies
577
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
20 months ago
Wolfgang Huber
★ 13k
1
vote
10
replies
1.9k
views
Obtaining pheno data from CEL files
GEO
affy
20 months ago
Kurtis
• 0
0
votes
1
reply
594
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
avery
• 0
1
vote
3
replies
921
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
1.5k
views
MethylKit read issue
methylKit
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
CHEN
• 0
1
vote
2
replies
5.3k
views
Extract genes from ggvenn?
ggvenn
updated 20 months ago by
Michael
▴ 10 • written 3.6 years ago by
axe880
• 0
0
votes
4
replies
914
views
Help with design.matrix
limma
20 months ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
720
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
20 months ago
andromeda
• 0
0
votes
2
replies
1.0k
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
joshua.mannheimer
• 0
2
votes
2
replies
943
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
614
views
Granges regionCounts not returning the expected number of entries
methylKit
20 months ago
Modoc Kesner
▴ 10
0
votes
0
replies
418
views
flowDensity on a flowset
flowDensity
20 months ago
fredrikwallberg
• 0
1
vote
1
reply
847
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Hong Thu
• 0
10
votes
41
replies
10k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 18 months ago by
Daniele
• 0 • written 7.0 years ago by
Guido Hooiveld
★ 4.1k
1
vote
3
replies
3.0k
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 14 months ago by
rania.alanany
• 0 • written 20 months ago by
Kim
• 0
0
votes
0
replies
668
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
20 months ago
Macsue
• 0
1
vote
4
replies
1.1k
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
jari.karppinen
• 0
3
votes
3
replies
16k
views
How to fix 'long vectors not supported yet' error in R
r
updated 20 months ago by
Amruta
• 0 • written 6.8 years ago by
r.tor
• 0
0
votes
2
replies
2.0k
views
error in install immunedeconv
Install
updated 20 months ago by
Arash
• 0 • written 2.7 years ago by
fenglingao
• 0
1
vote
6
replies
1.7k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 20 months ago by
Michael Love
43k • written 20 months ago by
RL
• 0
0
votes
2
replies
886
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
20 months ago
Gimena
• 0
0
votes
2
replies
944
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
20 months ago
Marianna
▴ 20
1
vote
6
replies
1.8k
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 20 months ago by
Tim Peters
▴ 230 • written 20 months ago by
s.malik
• 0
1
vote
1
reply
514
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 months ago
Layal
• 0
0
votes
2
replies
968
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
20 months ago
w.cookson
• 0
0
votes
2
replies
741
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
20 months ago
michelafrancesconi8
• 0
0
votes
1
reply
847
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Reeya
• 0
0
votes
4
replies
1.1k
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Aidan
• 0
0
votes
4
replies
1.5k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
20 months ago
Lucy
▴ 60
0
votes
1
reply
663
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Leyre
• 0
0
votes
2
replies
1.1k
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
20 months ago
Seongsu
• 0
0
votes
2
replies
889
views
Gene Ontology doubt
microbiomeExplorer
20 months ago
Bhawna
• 0
0
votes
1
reply
821
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 20 months ago by
Michael Love
43k • written 20 months ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
943
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
ja569116
• 0
0
votes
2
replies
835
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
20 months ago
fer_talavera
• 0
0
votes
7
replies
2.2k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 months ago
needNGS
• 0
46,691 results • Page
27 of 934
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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