0
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4
replies
1.1k
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
1
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2
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528
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Differential expression on the transcript-level
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updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
0
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3
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609
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
6 months ago Shajahan • 0
3
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13
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2.4k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
3
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2
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1.1k
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Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
639
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MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 6 months ago by 68k • written 6 months ago by • 0
0
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1
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1.0k
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Using offset in edgeR
edgeR
updated 6 months ago by 53k • written 6 months ago by • 0
2
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2
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ExperimentHub full metadata
ExperimentHub
written 7 months ago by ▴ 50
1
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2
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Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
1
reply
700
views
cytolib uses outdated boost call
cytolib
updated 6 months ago by 68k • written 6 months ago by • 0
4
votes
8
replies
2.0k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
2
replies
381
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can't post
devel
updated 6 months ago by 4.3k • written 6 months ago by • 0
7
votes
9
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5.8k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
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1
reply
1.5k
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 6 months ago by 53k • written 17.0 years ago by ▴ 10
0
votes
1
reply
599
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 months ago by 68k • written 6 months ago by • 0
3
votes
9
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4.8k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 3 months ago by • 0 • written 6 months ago by ▴ 10
1
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3
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2.5k
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Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 7 months ago by ▴ 10
0
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3
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2.5k
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 7 months ago by 53k • written 7 months ago by • 0
2
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4
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3.5k
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I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis lncRNA
7 months ago John ▴ 10
0
votes
2
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1.1k
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gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
0
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3
replies
1.8k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 7 months ago by 68k • written 7 months ago by • 0
5
votes
11
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3.9k
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parameters of filterByExpr
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written 9 months ago by ▴ 10
0
votes
5
replies
2.1k
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compute_fasta_digest does not match Salmon index hash
tximeta
written 10 months ago by • 0
0
votes
5
replies
1.0k
views
WGCNA
WGCNA Normalization RNASeq
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3
votes
4
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5.5k
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Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
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updated 7 months ago by 68k • written 7 months ago by ▴ 10
0
votes
3
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1.2k
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TopGO question
topGO top
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
2
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1.1k
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Starting with a clean bioconductor rstudio container
Bioconductor
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
2
replies
612
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
vote
5
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Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 6 months ago by 43k • written 7 months ago by • 0
0
votes
1
reply
781
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
1
reply
2.3k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
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updated 7 months ago by 43k • written 7 months ago by • 0
0
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2
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
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3
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1.1k
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 7 months ago by • 0 • written 7 months ago by • 0
1
vote
2
replies
3.9k
views
Is voomByGroup available in limma?
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7 months ago richardallenfriedmanbrooklyn ▴ 30
0
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4
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1.9k
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How to use goana function with zebrafish genome from org.Dr.eg.db
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7 months ago Eric • 0
1
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3
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1.5k
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News: Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt ensembldb
written 9 months ago by ▴ 30
0
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0
replies
25
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Spam: wealthdt5
weaver wealth
7 months ago Enfurry 0
0
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0
replies
324
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Y-axis break ihn Volcano Plot
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7 months ago rajdeepboral00 • 0
0
votes
0
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309
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getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC hcg110.db
updated 7 months ago by 4.3k • written 7 months ago by • 0
3
votes
2
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1.5k
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Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
1
vote
2
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by • 0
0
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0
replies
338
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Job: Job: Ensembl Dataflow Coordinator
JobPosting ensembldb
7 months ago Aleena_Ensembl ▴ 30
0
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1
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1.4k
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Retrieve Salmon transcript quantification file from recount3
recount3
updated 7 months ago by ★ 1.1k • written 8 months ago by ▴ 10
0
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1
reply
1.2k
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error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25 hcg110.db
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
1
reply
935
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Source / binary version mismatch for rGADEM
rGADEM
updated 7 months ago by 4.3k • written 8 months ago by • 0
0
votes
9
replies
13k
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Bioconductor version cannot be validated
BiocManager Bioconductor
updated 8 months ago by • 0 • written 4.5 years ago by ▴ 10
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
votes
2
replies
1.3k
views
Interaction in Design Experimental
rnaseqGene
8 months ago Ferdinand David • 0
0
votes
0
replies
389
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Job: Lab Head positions at the WEHI, Melbourne, Australia
JobPosting Bioconductor
8 months ago Gordon Smyth 53k
1
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4
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Heatmap of the Count Matrix
rnaseqGene
updated 4 months ago by • 0 • written 8 months ago by • 0
1,000 results • Page 5 of 20
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Replies
Answer: Limma-voom sample weights and impact on DEG numbers by fawadsaafir • 0
<a href="https://deltaexecutoor.com/">delta apk</a> también conocido como Delta X, es una herramienta avanzada para ejecutar scripts perso…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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