3
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2
replies
1.4k
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Unable to convert Uniprot ID to Gene IDs using Biomart
biomaRt
3.5 years ago rohitsatyam102 ▴ 20
0
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0
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1.1k
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Plot of variable importance
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3.5 years ago Eddie • 0
0
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0
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668
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gscreend: Multiple T0 replicates
gscreend
3.5 years ago pk_labrador • 0
0
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2
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DESeq2 analysis has not been run for this contrast
R DiffBind
3.5 years ago Wang • 0
0
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0
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1.3k
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intron coordination and annotation
ChIPSeq
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
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1
reply
1.8k
views
WGCNA Export Eigengene Adjacency/Correlation values export
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updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
0
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1
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Annotation in pheatmap
pheatmap
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
0
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0
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CytoML: gatingset_to_flowjo() "Could not find files for the given pattern(s)" error
CytoML
3.5 years ago nmchavez • 0
1
vote
6
replies
2.0k
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Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
3.5 years ago BioInfoBeginnerrr • 0
0
votes
0
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1.3k
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
3.5 years ago eolson • 0
1
vote
3
replies
1.6k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
7
replies
3.0k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
9
replies
2.9k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 2.3 years ago by ▴ 10 • written 3.5 years ago by ▴ 10
2
votes
7
replies
3.0k
views
biomaRt error during getBM
biomaRt
updated 3.5 years ago by ★ 6.6k • written 3.5 years ago by • 0
1
vote
3
replies
2.8k
views
ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 14 months ago by 43k • written 3.5 years ago by • 0
2
votes
2
replies
1.8k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
1
reply
1.1k
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.5 years ago Tongjun • 0
1
vote
0
replies
1.1k
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Why does surrogate variable confound with variable given in mod?
sva
3.5 years ago shdam ▴ 10
1
vote
0
replies
1.3k
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News: Ensembl 107 has been released
ensembldb
3.5 years ago Aleena_Ensembl ▴ 30
2
votes
5
replies
1.9k
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MafH5.gnomAD.v3.1.2.GRCh38 omitted indels
GenomicScores
updated 3.3 years ago by ★ 3.4k • written 3.5 years ago by • 0
0
votes
1
reply
5.4k
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gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
vote
0
replies
1.0k
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
3.5 years ago hlee ▴ 10
1
vote
1
reply
1.1k
views
Weight Array Quality before of after applying variance filtering?
limma arrays genefilter
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 40
0
votes
0
replies
1.2k
views
News: Introduction to genomic data analysis with R and Bioconductor in Heidelberg, 12-13 September 2022
Workshop
3.5 years ago Laurent Gatto 1.6k
0
votes
1
reply
940
views
DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 30
1
vote
2
replies
3.3k
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DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.5 years ago ClaudiaE • 0
1
vote
12
replies
4.7k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 2.3 years ago by ★ 1.5k • written 3.5 years ago by • 0
1
vote
1
reply
681
views
Error message : DESeq2
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
votes
2
replies
1.2k
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
3.5 years ago raf4 ▴ 30
0
votes
1
reply
3.0k
views
setReadable function missing information in clusterProfiler
clusterProfiler
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
votes
1
reply
10k
views
using biomaRt to look up human gene symbols and map them to human ensembl ENSG IDs
biomaRt
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
1
reply
1.3k
views
DiffBind: dba.plotPCA() ellipse
PrincipalComponent DiffBind
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
1
vote
1
reply
982
views
result does not change after relevel
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
0
replies
717
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how to obtain the download number of a bioconductor package
badges
3.5 years ago zhilongjia • 0
0
votes
0
replies
1.1k
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ARACNe Sample Size
grndata GRN ARACNE WGCNA
3.5 years ago Harrsha • 0
0
votes
0
replies
1.7k
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.5 years ago Guandong Shang ▴ 40
0
votes
14
replies
6.5k
views
GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 3.3 years ago by • 0 • written 3.5 years ago by • 0
0
votes
0
replies
1.3k
views
Cannot Install genefilter
genefilter
3.5 years ago Francis • 0
1
vote
0
replies
965
views
Which algorithm would you use for the cell-cell communication analysis of bulk RNA seq datasets?
RNASeq
3.5 years ago curiousmind007 ▴ 10
2
votes
5
replies
3.1k
views
proteomics analysis
Proteomics analysis
updated 3.5 years ago by ▴ 100 • written 3.5 years ago by • 0
0
votes
1
reply
928
views
suggested additional study
curatedMetagenomicData
updated 3.5 years ago by ▴ 240 • written 3.5 years ago by • 0
2
votes
2
replies
1.2k
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU DRIMSeq
3.5 years ago wangziwei0010 ▴ 10
0
votes
1
reply
2.1k
views
Error with ropls when using oplsda: Error in svd(wwMN) : infinite or missing values in 'x'
ropls
3.5 years ago g0079 • 0
0
votes
0
replies
1.1k
views
biomaRt has encountered an unknown server error
biomaRt
3.5 years ago Grace_H • 0
0
votes
0
replies
876
views
Enrichment in genomic regions
Enrichment clusterPro WGCNA
3.5 years ago María José • 0
0
votes
4
replies
4.8k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 3.5 years ago by ▴ 760 • written 3.5 years ago by ▴ 30
0
votes
0
replies
1.2k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt customProDB
3.5 years ago 04.marshal-decibel • 0
1
vote
1
reply
2.7k
views
enrichGO results
clusterProfiler enrichGO
3.5 years ago Shakiba • 0
2
votes
2
replies
950
views
DESeq2 question
DESeq2
3.5 years ago Yu • 0
0
votes
4
replies
1.5k
views
Multi-factorial Time-based design in DEseq2: defining full and reduced model
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
46,730 results • Page 83 of 935
Recent ...
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
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