Showing : RnaSeq • reset
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Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
23 hours ago • updated 21 hours ago JAcky • 0
2
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2
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66
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Can't load UCSC transcript IDs
RNASeq
updated 6 days ago by ★ 3.3k • written 7 days ago by • 0
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103
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deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
7 days ago Victor • 0
3
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3
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132
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Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 7 days ago by 37k • written 18 days ago by • 0
0
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1
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77
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lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 14 days ago by ★ 1.3k • written 15 days ago by • 0
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1
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55
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Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 17 days ago by 37k • written 18 days ago by • 0
1
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1
reply
126
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RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 17 days ago by 37k • written 19 days ago by • 0
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1
reply
64
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NOIseq Probability column
RNAseq RNASeqData NOISeq
22 days ago • updated 11 days ago Pratibha • 0
3
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3
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167
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Limma vs deseq2 results
limma RNASeq R
28 days ago • updated 26 days ago k___ ▴ 20
3
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3
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167
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Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 5 weeks ago by 45k • written 5 weeks ago by ▴ 10
3
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6
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308
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Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
5 weeks ago andrebolerbarros ▴ 10
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2
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229
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Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 7 weeks ago by • 0
1
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1
reply
117
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Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 5 weeks ago by 45k • written 5 weeks ago by • 0
1
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2
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156
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 6 weeks ago by 37k • written 6 weeks ago by • 0
3
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11
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447
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RNA-seq: compare two technical replicates
RNASeq
updated 7 weeks ago by 45k • written 8 weeks ago by • 0
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2
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142
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edgeR
rnaseq edgeR
updated 9 weeks ago by 45k • written 9 weeks ago by • 0
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3
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176
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Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 9 weeks ago by ★ 1.1k • written 10 weeks ago by • 0
5
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6
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316
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Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
10 weeks ago Alan • 0
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0
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92
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
10 weeks ago chiwut.wong • 0
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0
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82
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
11 weeks ago OST • 0
2
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4
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208
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confused with tximport counts abundance using salmon input
RNASeq tximport
11 weeks ago Al90 • 0
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7
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349
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DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 10 weeks ago by 37k • written 11 weeks ago by • 0
0
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1
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184
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Rtracklayer
rtracklayer RNASeq gff
updated 12 weeks ago by 60k • written 12 weeks ago by • 0
0
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1
reply
150
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 12 weeks ago by 37k • written 12 weeks ago by • 0
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3
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184
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DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3 months ago by 37k • written 3 months ago by • 0
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2
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1.7k
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DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3 months ago by • 0 • written 5.8 years ago by ▴ 40
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0
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120
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3 months ago treebig44 ▴ 30
1
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0
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94
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Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery RNASeq
3 months ago Liliian • 0
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0
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212
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Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3 months ago Raito92 ▴ 60
2
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2
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174
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Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 3 months ago by 45k • written 3 months ago by ▴ 60
0
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4
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252
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limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
3 months ago danphillips28 • 0
0
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1
reply
164
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GSEA using custom GO annotations
RNASeq GSEA
updated 3 months ago by ★ 2.9k • written 3 months ago by • 0
0
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1
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181
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Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 3 months ago by 45k • written 3 months ago by • 0
4
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1
reply
224
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3 months ago by 37k • written 3 months ago by ▴ 30
1
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1
reply
119
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3 months ago by 37k • written 3 months ago by ▴ 30
2
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6
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332
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3 months ago treebig44 ▴ 30
0
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0
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118
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3 months ago by 37k • written 3 months ago by • 0
2
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2
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208
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Complex contrasts in limma
RNASeq limma DifferentialExpression
3 months ago tcalvo ▴ 70
0
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2
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216
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Differential expression in fixed windows
DESeq2 RNASeq
4 months ago anatmela • 0
2
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1
reply
224
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DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 4 months ago by 37k • written 4 months ago by • 0
0
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1
reply
170
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Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 4 months ago by 37k • written 4 months ago by • 0
0
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1
reply
216
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95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
0
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1
reply
206
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Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 4 months ago by 60k • written 4 months ago by • 0
0
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4
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362
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How do you get averages of each group in Limma output
RNASeq limma
4 months ago Matthew • 0
0
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6
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496
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 4 months ago by 37k • written 4 months ago by ▴ 60
0
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4
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361
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Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 5 months ago by ★ 1.1k • written 5 months ago by • 0
0
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3
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405
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DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 5 months ago by ▴ 330 • written 5 months ago by • 0
0
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3
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469
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using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 5 months ago by 45k • written 5 months ago by ▴ 70
1
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2
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204
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 5 months ago by 37k • written 5 months ago by • 0
0
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2
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222
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
5 months ago IamFrofro • 0
50 results • Page 1 of 1
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Comment: Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelih by ATpoint ★ 1.3k
Would you mind reading the vignette towards how the LRT works: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2…
Comment: cellCounts() function floating point error by Yang Liao ▴ 340
Thanks for the report but the error cannot be reproduced. We tested `Rsubread` 2.10.3 in `R` 4.2.0 and `Bioconductor` 3.15, and `cellCounts…
Comment: rtracklayer export GRangesList as gtf and change attributes by James • 0
I have found a way to export a GTF so that the 3rd column no longer lists **sequence_feature** but instead lists the feature, such as **exo…
Comment: Using Age or other numerical variable to model expression in deseq2 by swbarnes2 ★ 1.1k
You can import age and not make it a factor.
Comment: Using Age or other numerical variable to model expression in deseq2 by krushnach80 • 0
"Why is that" no as an example i was citing that.."certainly don't want to make the interaction between the nuisance variable and your vari…
Votes
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
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