Showing : DESeq • reset
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 330
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3
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DESeq multifactor design paired analysis
DESeq DESeq
12.5 years ago Natasha ▴ 440
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4
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6.0k
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DESeq Variance Stabilizing Transformation
Clustering DESeq DESeq2 Clustering DESeq DESeq2
updated 12.5 years ago by 43k • written 12.5 years ago by ▴ 50
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2
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DESeq Normalization Question
Normalization DESeq Normalization DESeq
updated 12.5 years ago by ★ 7.9k • written 12.5 years ago by ▴ 290
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7
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heatmap with variance stabilizing transformed expression data in DESeq
DESeq DESeq
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 180
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2
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DEXSeq: subsetting ExonCountSet ?
DESeq DEXSeq DESeq DEXSeq
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 50
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1
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1.0k
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A few questions about DESeq2 (estimation of dispersion and results table)
DESeq DESeq2 DESeq DESeq2
updated 12.6 years ago by 43k • written 12.6 years ago by ▴ 80
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1
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776
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FW: DESeq Design (val1 vs mean (val2, val3, val4))
DESeq DESeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 20
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3
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DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
Normalization DESeq DEXSeq Normalization DESeq DEXSeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 40
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RNAseq analyses: to use, or not use, all the samples; that's the question.
PROcess edgeR DESeq PROcess edgeR DESeq
12.6 years ago Aaron Mackey ▴ 200
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3
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4.4k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 330
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1
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1.2k
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EdgeR- how to work PARTIALLY without replicates
edgeR DESeq edgeR DESeq
updated 12.6 years ago by 53k • written 12.6 years ago by ▴ 10
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1
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3.0k
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DESeq: computing 95% CI for negative binomial distribution ?
TimeCourse timecourse DESeq TimeCourse timecourse DESeq
updated 12.6 years ago by 43k • written 12.6 years ago by ▴ 50
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1
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1.3k
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DESeq: computing 95% CI for negative binomial distribution ?
DESeq DESeq
updated 12.6 years ago by 43k • written 12.6 years ago by ▴ 50
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1.2k
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deseq2
DESeq DESeq2 DESeq DESeq2
12.6 years ago Michael Love 43k
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4
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9.8k
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rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ★ 13k
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10
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2.7k
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Multifactor analysis with deseq
Normalization DESeq DESeq2 Normalization DESeq DESeq2
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 420
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14
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3.3k
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(no subject)
DESeq DESeq
updated 12.7 years ago by ▴ 20 • written 12.7 years ago by ▴ 30
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5
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3.9k
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DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 12.7 years ago by 43k • written 12.7 years ago by ★ 13k
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7
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14k
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Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 4.6 years ago by • 0 • written 12.7 years ago by ▴ 30
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1
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1.2k
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DESeq pairwise comparisons between conditions within a multi-factor design
DESeq DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 10
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2
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1.8k
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Difference between EdgeR and DeSeq in library normalization
RNASeq Normalization edgeR DESeq RNASeq Normalization edgeR DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 330
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3
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DESeq - plotPCA
DESeq DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ★ 13k
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1
reply
1.6k
views
DESeq Design issue
DESeq DESeq
updated 12.8 years ago by ★ 3.8k • written 12.8 years ago by ★ 13k
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6
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2.5k
views
Log transformation and left censoring
limma edgeR DESeq limma edgeR DESeq
updated 12.8 years ago by 53k • written 12.8 years ago by ★ 13k
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3
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1.9k
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Getting DESEq results on just one gene
DESeq DESeq
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 320
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3
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1.5k
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DEXSeq: building exon count set
DESeq DEXSeq DESeq DEXSeq
updated 12.8 years ago by ★ 1.9k • written 12.8 years ago by ▴ 140
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1
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1.6k
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DESeq - working with more than 2 conditions
DESeq DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ▴ 20
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4
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1.2k
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DESeq package error
DESeq DESeq
updated 12.9 years ago by ★ 8.2k • written 12.9 years ago by ▴ 30
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1
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2.1k
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GLM in DEseq
DESeq DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ★ 13k
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5
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2.0k
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filtering before using DESeq
DESeq DESeq
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 190
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2
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2.7k
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DESeq and EdgeR log fold differences
Normalization edgeR DESeq Normalization edgeR DESeq
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 40
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1
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1.7k
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DESeq: GLM for multi-factor and mulit-level designs
DESeq DESeq
updated 13.0 years ago by ★ 7.9k • written 13.0 years ago by ▴ 60
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1
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1.4k
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Experimental design with edgeR and DESeq packages (RNA-seq)
edgeR DESeq edgeR DESeq
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 50
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1
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1.0k
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DESeq not available
DESeq DESeq
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ★ 13k
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7
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5.2k
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edgeR/DESeq for ChIP-seq analysis
edgeR DESeq edgeR DESeq
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 240
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6
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Is there any prejudice whether to use edgeR or DESeq for differential expression analysis for RNA Seq data
edgeR DESeq edgeR DESeq
updated 13.0 years ago by ▴ 880 • written 13.0 years ago by ▴ 40
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0
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1.4k
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Removing overlapping genes from annotation for RNAseq read count
RNASeq Annotation PROcess DESeq RNASeq Annotation PROcess DESeq
13.0 years ago Guest User ★ 13k
2
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1
reply
2.2k
views
DESeq package
Proteomics DESeq Proteomics DESeq
updated 13.1 years ago by ▴ 550 • written 13.1 years ago by ▴ 20
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654
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Multi-factor designs with specific comparisons
DESeq DESeq
13.1 years ago Guest User ★ 13k
0
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1
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3.8k
views
mixed-effects analysis within DEseq
RNASeq DESeq RNASeq DESeq
updated 13.1 years ago by ▴ 150 • written 13.1 years ago by ▴ 10
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4
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1.8k
views
DESeq diagnostics
RNASeq Normalization DESeq RNASeq Normalization DESeq
updated 13.1 years ago by ★ 13k • written 13.1 years ago by ▴ 100
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1
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2.9k
views
plotPCA error
RNASeq DESeq RNASeq DESeq
updated 13.1 years ago by ★ 13k • written 13.1 years ago by ★ 13k
0
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4
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1.5k
views
(no subject)
RNASeq Normalization GO DESeq RNASeq Normalization GO DESeq
updated 13.1 years ago by ★ 2.0k • written 13.1 years ago by ▴ 100
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0
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1.2k
views
DESeq - skewed MAplots and other problems
RNASeq Normalization GO DESeq RNASeq Normalization GO DESeq
13.1 years ago Michal Lulu ▴ 100
0
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12
replies
4.0k
views
DEseq version and R version compatibility
DESeq DESeq
updated 13.1 years ago by ★ 1.7k • written 13.1 years ago by ▴ 280
0
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0
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949
views
ANOVA in edgeR?
edgeR DESeq edgeR DESeq
13.1 years ago Gordon Smyth 53k
0
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5
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1.0k
views
shan
DESeq DESeq
updated 13.1 years ago by ★ 13k • written 13.1 years ago by ★ 2.0k
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0
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950
views
DESeq plotting graphs.
DESeq DESeq
13.1 years ago PRAVIN ▴ 10
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2
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1.7k
views
DESeq - working with more than 2 conditions
edgeR DESeq edgeR DESeq
updated 13.1 years ago by ▴ 180 • written 13.1 years ago by ▴ 440
512 results • Page 7 of 11
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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