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3
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5.4 years ago TriS ▴ 200
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2
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updated 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
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updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 40
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8
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Differential gene expression using R
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updated 5.4 years ago by 53k • written 5.4 years ago by • 0
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Getting rs ids using chr coordinates | Biomart
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updated 2.5 years ago by 68k • written 5.4 years ago by • 0
1
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Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
0
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1
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1.8k
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gsva
updated 5.4 years ago by ★ 3.4k • written 5.4 years ago by • 0
1
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CEMiTool: error in overrepresentation analysis (Enrichment is null)/mod_ora function
CEMiTool
updated 5.1 years ago by ▴ 30 • written 5.4 years ago by ▴ 10
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2
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maSigPro: PlotGroups function only plots one out of six time points
maSigPro PlotGroups
updated 24 months ago by • 0 • written 5.4 years ago by • 0
0
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1.1k
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DE analysis packages not detecting Splat DE simulated genes
splatter
updated 5.4 years ago by ▴ 50 • written 5.4 years ago by • 0
0
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How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 30
3
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2
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3.1k
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lfcShrink function in DEseq2 and s-values
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
0
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2
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updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 80
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droplevels not working - error in DESeq() function
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5.4 years ago DcL-A • 0
1
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3
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updated 5.4 years ago by ★ 1.6k • written 5.5 years ago by ▴ 10
1
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3
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
8
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4
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Tidyverse can be a bit tidiest to work with....
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updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 30
1
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0
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Job: Postdoc/Bioinformatician Research Fellow @ Harvard Medical School/MGH/ Boston's Children Hospital
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5.4 years ago bauer ▴ 10
0
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0
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2.0k
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Job: Scientist 1, Bioinformatics (Research | Berkeley, CA | Full Time)
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5.4 years ago yzhang • 0
2
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4
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Trajectory analysis for single cell sequencing
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updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
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4
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updated 5.4 years ago by • 0 • written 5.4 years ago by ▴ 20
0
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2.5k
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predicting cell type of clusters using singleR
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updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
1
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2
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can eBayes be used with inverse normalized expression levels?
limma
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3
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0
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SELEX: Rookie mistake (solved)
java selex barcode
5.4 years ago jeleo • 0
0
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1
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492
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DESeq2 differentially expressed genes
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updated 5.4 years ago by 43k • written 5.4 years ago by • 0
7
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8
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Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
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updated 5.4 years ago by 43k • written 5.4 years ago by • 0
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5
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isoform data, deep sequencing and voom
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updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 620
1
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1
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Can I add raw counts for duplicated genes?
DESeq2 RNAseq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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5
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Error using DRIMSeq with Salmon count data
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updated 5.4 years ago by 43k • written 5.4 years ago by • 0
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12
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Error Message in DESEQ (DESEQDataSetFromMatrix)
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
2
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updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
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how to suppress makeVennDiagram plot
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5.4 years ago C T ▴ 140
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
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updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
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updated 5.4 years ago by 68k • written 5.4 years ago by • 0
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Error in .local(x, i, j = j, ...) : 'i' must be length 1 in using OrganismDbi to create org.XX.eg.db
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updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 20
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updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 50
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ensembl to hgnc symbols creates duplicates
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updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 60
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Missing Point in PCA Analysis
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updated 5.4 years ago by 43k • written 5.4 years ago by • 0
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updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
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11
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Is there any model in EdgeR that is close to nested ANOVA?
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updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 10
2
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Parsing geoms to enrichplot
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5.4 years ago Francois Marchildon ▴ 20
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RSEM for DESeq2 without abundance matrix
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
0
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713
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Obtaining expanded model matrices when using apeglm
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updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
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2
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updated 5.4 years ago by ★ 4.0k • written 5.5 years ago by ▴ 60
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1
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Help installing depmap on R 3.6.3
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2
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"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
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updated 5.5 years ago by ★ 6.6k • written 5.5 years ago by • 0
46,726 results • Page 157 of 935
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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…
Votes
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
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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