0
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0
replies
1.4k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
3.5 years ago qiz218591 • 0
5
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9
replies
3.1k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
3.5 years ago Yang Shi ▴ 10
1
vote
7
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3.7k
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Error with slingshot slingPseudotime and slingCurveWeights after using fitGAM from tradeSeq
tradeSeq slingshot
3.5 years ago manduchi ▴ 10
0
votes
1
reply
3.0k
views
Bioconductor will not install on Rstudio
ALL
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
vote
2
replies
2.1k
views
I want to know how to analyze TCGA data with maftools.
TCGAWorkflowData
updated 3.4 years ago by 700 • written 3.5 years ago by • 0
0
votes
1
reply
1.5k
views
error in champ.SVD() "Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : subscript out of bounds"
Hi
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
0
votes
1
reply
1.3k
views
Attempt to install bioconductor 3.15, PCAtools
PCAtools bioconductor
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
vote
1
reply
960
views
IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
1
reply
1.1k
views
Regarding Installation of GEOquery
BiocManager installation GEOquery
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
0
votes
3
replies
1.8k
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
3.5 years ago marius.wenzel • 0
1
vote
2
replies
2.3k
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
3.5 years ago fluentin44 • 0
0
votes
1
reply
1.4k
views
Help with featureCounts
DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
3
votes
2
replies
1.5k
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
3.5 years ago manwar • 0
0
votes
0
replies
1.1k
views
TCGAbiolinks file.type argument
TCGAbiolinks
3.5 years ago Elizabeth • 0
2
votes
2
replies
2.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.5 years ago Yang Shi ▴ 10
0
votes
0
replies
1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.5 years ago Sebastian Lewandowski • 0
0
votes
1
reply
1.5k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.5 years ago Jenny Drnevich ★ 2.0k
1
vote
4
replies
2.1k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.5 years ago Chise ▴ 10
0
votes
0
replies
982
views
Displaying large image stacks (e.g. from multiplexed immunohistochemistry) using shiny and EBImage
shiny EBImage
3.5 years ago Wolfgang Huber ★ 13k
0
votes
8
replies
4.9k
views
DESeq2 different log2FC and p-value filtering parameters results comparison
log2 DESeq2
3.5 years ago User000 • 0
0
votes
3
replies
7.8k
views
ridgeplot doesn't work: Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : replacement has length zero
clusterProfiler
updated 3.3 years ago by • 0 • written 3.5 years ago by • 0
0
votes
0
replies
799
views
biomaRt, Ensembl, adding new "phenotype_source"
biomaRt
3.5 years ago Hector • 0
2
votes
4
replies
2.2k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
0
votes
0
replies
935
views
Plotting a line plot for genes across 4-species
RNAseq123
3.5 years ago Mohamed ▴ 30
0
votes
3
replies
1.9k
views
cn.mops segmentation error
cn.mops
updated 3.4 years ago by • 0 • written 3.5 years ago by ▴ 40
5
votes
6
replies
2.8k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.5 years ago Yang Shi ▴ 10
0
votes
8
replies
3.1k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 3.2 years ago by • 0 • written 3.5 years ago by • 0
4
votes
2
replies
1.2k
views
good-first-issue (or similar) GitHub
Culture R GitHub
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
1
reply
1.2k
views
DESeq normalization
flowCHIC
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
votes
4
replies
2.8k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.5 years ago Yang Shi ▴ 10
7
votes
6
replies
2.2k
views
BiocStyle::html_document does not render Glimma plots
Glimma BiocStyle
updated 3.5 years ago by ★ 6.6k • written 3.5 years ago by ▴ 30
1
vote
5
replies
1.5k
views
DeSeq2 Matched Analysis
RNASeq DESeq2
3.5 years ago Andrea • 0
2
votes
9
replies
2.6k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
0
replies
864
views
Negative Q2Y
Metabolomics
3.5 years ago Eddie • 0
2
votes
2
replies
1.8k
views
Unable to download CATALYST
CATALYST
3.5 years ago David • 0
0
votes
3
replies
3.4k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
1
reply
2.3k
views
Unable to access index for Bioconductor repository
Monterey macOS Bioconductor
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by • 0
0
votes
0
replies
992
views
MetaVolcanoR usage
limma MetaVolcanoR EnhancedVolcano
3.5 years ago JAcky • 0
0
votes
0
replies
818
views
Filtering references to a taxa
brendaDb
3.5 years ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
2.9k
views
[DESeq2] setting LFC threshold
DESeq2
3.5 years ago Shail • 0
0
votes
1
reply
1.9k
views
lfcShrink types for Volcano plots
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
3
votes
4
replies
1.6k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.5 years ago Yang Shi ▴ 10
0
votes
1
reply
829
views
DESeq2: correct way to extract comparison of comparisons
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
1
reply
615
views
DESeq2 for CaptureSeq
CaptureSeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
1
reply
1.7k
views
GViz plot coverage for multiple chromosome and multiple samples using BAM files and save them as a single pdf report
Gviz
3.5 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
1.4k
views
Unable to convert Uniprot ID to Gene IDs using Biomart
biomaRt
3.5 years ago rohitsatyam102 ▴ 20
0
votes
0
replies
1.1k
views
Plot of variable importance
Metabolomics
3.5 years ago Eddie • 0
0
votes
0
replies
666
views
gscreend: Multiple T0 replicates
gscreend
3.5 years ago pk_labrador • 0
0
votes
2
replies
1.5k
views
DESeq2 analysis has not been run for this contrast
R DiffBind
3.5 years ago Wang • 0
0
votes
0
replies
1.3k
views
intron coordination and annotation
ChIPSeq
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
46,725 results • Page 82 of 935
Recent ...
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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