Showing : RNA-SEQ • reset
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Paired design, normalisation and batch effects.
deseq2 eda sva rna-seq
updated 9.2 years ago by ▴ 610 • written 9.2 years ago by ▴ 10
0
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1
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1.3k
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Question on Gage
gage package path.ids RNA-Seq
9.2 years ago rl1385 • 0
10
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4
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5.5k
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Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 110
0
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3
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2.4k
views
DESeq2 time course experiments for multigroups comparison (>2 groups)
DESeq2 Time course RNA-seq
updated 9.3 years ago by 43k • written 9.3 years ago by ▴ 40
3
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4
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2.0k
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Cannot install CummeRbund on R v.3.3.0
cummeRbund RNA-Seq
9.3 years ago eihpos76mm • 0
12
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2
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4.1k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 80
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1
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943
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Is there any R package taking care of random effect for RNA-Seq read counts gene expression data
rna-seq
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 120
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2
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2.0k
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Error trying to load counts matrix and lane information using "newSeqExpressionSet"
edaseq error rna-seq normalization
updated 9.3 years ago by ▴ 980 • written 9.3 years ago by • 0
0
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0
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940
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Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
limma microarray rna-seq
9.3 years ago Thomas.F.Hahn2 • 0
0
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0
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1.3k
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Job: Remote bioinformatics assistance for severely visually impaired bioinformatics graduate student needed
microarray limma affymetrix microarrays r microarray affy rna-seq Job
9.3 years ago Thomas.F.Hahn2 • 0
2
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0
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1.5k
views
Job: Two Post-doctoral positions at the CRUK Cambridge Institute
cancer methylation rna-seq Job
9.3 years ago Andy Lynch ▴ 120
0
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3
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1.9k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
9.4 years ago newsomew13 • 0
4
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5
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6.9k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 9.4 years ago by ★ 3.6k • written 9.4 years ago by ▴ 180
1
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3
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1.8k
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How to resolve length bias and get GO/KEGG pathway for "non-standard" species in limma or goseq ?
rna-seq limma goseq
updated 9.4 years ago by ▴ 320 • written 9.4 years ago by ▴ 40
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3
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3.2k
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DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 9.4 years ago by ★ 13k • written 9.4 years ago by • 0
0
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0
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1.7k
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
9.4 years ago Katja Hebestreit ▴ 130
0
votes
1
reply
1.3k
views
Functions of DESeq2 package
deseq2 differential gene expression rna-seq
updated 9.5 years ago by ★ 13k • written 9.5 years ago by • 0
1
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13
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7.4k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
9.5 years ago gil.hornung • 0
5
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7
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2.0k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 9.5 years ago by ★ 29k • written 9.5 years ago by ▴ 10
3
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3
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1.5k
views
RNA-seq genes differentially expressed in combined treatment
DESeq2 deseq2 RNA-seq
9.5 years ago david.ashbrook • 0
3
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4
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2.0k
views
how to use edgeR analysis RNA-seq data with a obvious deviation sample
edger RNA-seq anova
updated 9.5 years ago by ★ 29k • written 9.5 years ago by • 0
3
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7
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5.1k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 90
1
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5
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1.6k
views
Question about contrast matrix using limma
limma rna-seq limma contrast matrix
updated 9.5 years ago by 53k • written 9.5 years ago by • 0
0
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2
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5.3k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
0
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3
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1.9k
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Calculating a score from fold change matrix of pair-wise rna-seq data
rna-seq deseq2 differential gene expression biostatistics
9.5 years ago g.atla ▴ 10
2
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10
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2.7k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
9.6 years ago Yogender Gowtham ▴ 20
2
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1
reply
1.5k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq edgeR limma removebatcheffect() batch
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 80
0
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2
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5.9k
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WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 10
0
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2
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1.6k
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DEXSeq on time series - how to set up models
DEXSeq timecourse rna-seq differential exon usage
updated 9.6 years ago by ★ 1.9k • written 9.6 years ago by • 0
4
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11
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3.1k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 10
24
votes
11
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21k
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when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 50
1
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3
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1.4k
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DESeq2 Finding genotype effect to stimulation minus effect of not stimulating
deseq2 rna-seq
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 60
0
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2
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3.3k
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WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.7 years ago hywel.williams • 0
5
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5
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1.8k
views
edgeR no residual degrees of freedom for a specific row of numbers in dispCoxReidInterpolateTagwise
edger rna-seq
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 180
0
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1
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1.5k
views
Error with SCAN.UPC UPC_RNASeq method
scan.upc RNA-Seq UPC
9.8 years ago vn • 0
3
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5
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2.5k
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How to handle mix of samples from the same subject and from different subjects during differential expression analysis of RNA-seq using GLMs?
rnaseq rna-seq differential gene expression differential expression edger
updated 9.8 years ago by ★ 7.9k • written 9.8 years ago by ▴ 70
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2
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3.3k
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DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
9.8 years ago erin.gill81 ▴ 60
4
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2
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3.0k
views
Quality control on RNA-Seq (level 3) data from TCGA
rna-seq GC-Content qualitycontrol
updated 9.9 years ago by ▴ 180 • written 9.9 years ago by ▴ 60
1
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1
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2.0k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 9.9 years ago by ★ 29k • written 9.9 years ago by • 0
1
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1
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1.5k
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EBSeq-HMM: retrieving expression paths for genes differing by time AND treatment
ebseq ebseq-hmm rna-seq
9.9 years ago vieuphoria ▴ 10
9
votes
1
reply
3.6k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 130
1
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1
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3.4k
views
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
deconvolution rna-seq
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 160
3
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4
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3.6k
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Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse time course rna-seq deseq2 ggplot2
10.1 years ago moldach ▴ 20
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0
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2.1k
views
Job: Research Scientist in Bioinformatics/Statistical Genomics, Max Planck Institute, Nijmegen, Netherlands
job rnaseq rna-seq genomics data integration Job
10.1 years ago clyde.francks • 0
2
votes
9
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2.6k
views
i can't find cummeRbund package
software error cuumeRbund rna-seq
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 40
5
votes
3
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3.8k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 30
5
votes
5
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2.0k
views
Extract specific contrast from paired multifactor design matrix
edger deseq2 rna-seq
updated 10.2 years ago by 68k • written 10.2 years ago by ★ 2.1k
9
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12
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9.2k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 17 months ago by • 0 • written 10.2 years ago by ▴ 30
3
votes
6
replies
4.5k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 10.3 years ago by 53k • written 10.3 years ago by ▴ 60
18
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12
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4.7k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 10.3 years ago by 43k • written 10.3 years ago by ★ 7.9k
418 results • Page 8 of 9
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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