Showing : RNA-Seq • reset
0
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4
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927
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DESeq2 nested effect with 5 variables
deseq2 RNA-seq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.5 years ago by 53k • written 7.1 years ago by • 0
5
votes
11
replies
4.6k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
6.7 years ago • updated 6.5 years ago pierre.marin • 0
0
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5
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2.8k
views
RNA-seq time course analysis with only one experimental condition
deseq2 cancer rna-seq time-series
6.5 years ago mah19 • 0
1
vote
9
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3.5k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
0
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0
replies
1.1k
views
arrayQualityMetrics with count table of RNA-Seq data - how to make ExpressionSetobject or ExpressionSetIllumina object?
arrayQualityMetrics RNA-Seq ExpressionSetobject ExpressionSetIllumina
6.6 years ago Mabeyer • 0
5
votes
3
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2.0k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
1
vote
12
replies
2.2k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 90
2
votes
2
replies
1.5k
views
voomWithQualityWeights together with covariate in design matrix
limma voom RNA-seq voomWithQualityWeights
updated 6.6 years ago by ▴ 1000 • written 6.7 years ago by ▴ 90
4
votes
1
reply
1.4k
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 6.7 years ago by ★ 1.9k • written 6.7 years ago by ▴ 10
0
votes
10
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3.5k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 6.8 years ago by • 0
2
votes
5
replies
1.5k
views
Software package for RNA-seq reads simulation?
rna-seq reads
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 100
0
votes
2
replies
972
views
Can EDGE analyse RNA-seq data?
edge RNA-seq
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
2
votes
3
replies
1.6k
views
RNA-Seq Workflow Example (not "airway") for R
RNA-Seq Workflow
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
2
votes
1
reply
2.2k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
votes
2
replies
1.2k
views
DESeq2 for differential expression between species
deseq2 rna-seq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
1.1k
views
advice on exosome RNA-seq analysis
exosome rna-seq
6.7 years ago adai • 0
0
votes
2
replies
1.4k
views
Celaref error relating to MAST DE ananlysis
software error celaref single cell RNA-seq
updated 6.7 years ago by ▴ 40 • written 6.7 years ago by • 0
1
vote
2
replies
1.5k
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 6.7 years ago by ▴ 160 • written 6.7 years ago by ▴ 60
0
votes
1
reply
1.7k
views
random effects + interaction term + limma
random effects interaction limma rna-seq
6.7 years ago flippy23 • 0
7
votes
4
replies
5.3k
views
Minimum number of samples per treatment/group for WGCNA analysis
WGCNA RNA-seq GCN gene coexpression network
updated 6.7 years ago by ▴ 20 • written 6.7 years ago by ▴ 50
2
votes
5
replies
1.4k
views
Deseq2 Multivariate Time Series: DEGs for each time point comparison?
deseq2 RNA-seq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
1
reply
1.4k
views
Analyzing (HiSeq) PANCAN data set RNA-seq data using DaMiRseq
DaMiR RNA-seq software error DaMiRseq
6.7 years ago Daedalus99 • 0
5
votes
7
replies
3.5k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 20
2
votes
5
replies
3.5k
views
MDS plot; Batch effects
limma rna-seq edger batches
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
DESeq2 Design for 2 Conditions
deseq2 r R RNA-Seq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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0
replies
1.1k
views
Estimating sample size for specific platforms
software error RnaSeqSampleSize r RNA-seq
6.8 years ago AZ ▴ 20
0
votes
11
replies
2.3k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
6.8 years ago saddamhusain77 • 0
0
votes
1
reply
1.5k
views
Index genome generation with Subread for colorspace data
subread solid-seq data colorspace rna-seq
updated 6.8 years ago by ▴ 450 • written 6.8 years ago by • 0
2
votes
8
replies
2.9k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
votes
1
reply
606
views
Adding samples data from different experiment
rna-seq deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 60
0
votes
1
reply
2.3k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 4.5 years ago by 53k • written 6.8 years ago by • 0
2
votes
2
replies
1.3k
views
Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 6.8 years ago by ▴ 180 • written 6.8 years ago by ▴ 10
2
votes
3
replies
2.3k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 6.8 years ago by ★ 13k • written 6.8 years ago by ▴ 20
0
votes
3
replies
1.4k
views
model design in rna seq - deseq2
deseq2 rna-seq variability model-design
6.9 years ago • updated 6.8 years ago acebolladaso.iacs • 0
5
votes
5
replies
8.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 60
2
votes
10
replies
2.8k
views
Coseq error with DESeq2 object: Error in "normFactors"
coseq rna-seq
updated 6.9 years ago by ▴ 80 • written 6.9 years ago by • 0
0
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4
replies
1.5k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 20
3
votes
3
replies
3.2k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.9 years ago by ★ 3.0k • written 6.9 years ago by ▴ 60
4
votes
6
replies
4.7k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 70
0
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1
reply
1.0k
views
Local versus parametric fitType in DESeq2 in this instance?
deseq2 rna-seq
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
3
replies
4.5k
views
Differences in contrast results while using DESeq2 for one vs all rest combined conditions
deseq2 rna-seq differential expression analysis
6.9 years ago shreygandhi1990 ▴ 10
2
votes
3
replies
1.8k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.9 years ago by ★ 6.6k • written 7.0 years ago by ▴ 80
3
votes
2
replies
1.6k
views
ASpli readCounts never ends!
aspli readCounts rna-seq alternative splicing AS
7.0 years ago fernandalpcosta ▴ 10
3
votes
2
replies
3.1k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq featureCounts STAR minMQS mapping quality score
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 20
2
votes
4
replies
3.6k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 60
1
vote
5
replies
1.8k
views
My linear regression model is giving me too many differentially expressed genes
limma rna-seq differential gene expression edger linear regression
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
2
votes
5
replies
2.4k
views
edgeR or wilcoxon rank test? Which is right?
edgeR r wilcox RNA-seq cancer
7.0 years ago AZ ▴ 20
2
votes
1
reply
2.8k
views
How to change stringtie gene_id names with ref_gene_id when performing featureCount
featureCount rna-seq gene_id re_gene_id stringtie
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by • 0
2
votes
3
replies
1.6k
views
How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression enrichment RNA-seq DESeq2
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 40
418 results • Page 4 of 9
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Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
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Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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