Showing : DESeq • reset
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DESeq nbinomGLMTest specific comparisons
DESeq DESeq2 DESeq DESeq2
updated 11.9 years ago by ★ 7.9k • written 11.9 years ago by ▴ 40
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diffbind question : bSubControl with DEseq
DESeq DiffBind DESeq DiffBind
11.9 years ago Rory Stark ★ 5.2k
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1
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643
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Using DESeq to test for null ratios other than 1:1
DESeq DESeq
updated 11.9 years ago by ★ 3.8k • written 11.9 years ago by ★ 13k
0
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1
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869
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DESeq problem
DESeq DESeq
updated 12.0 years ago by ▴ 540 • written 12.0 years ago by ★ 13k
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1
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1.7k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 12.0 years ago by ▴ 320 • written 12.0 years ago by 53k
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1.5k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
12.0 years ago Nicolas Delhomme ▴ 320
0
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1
reply
817
views
DESeq nbinomGLMTest specific comparisons
DESeq DESeq
updated 12.0 years ago by ★ 13k • written 12.0 years ago by ▴ 40
0
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2
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3.1k
views
DESeq warning: "Dispersion fit did not converge" with replicates counts data
DESeq DESeq2 DESeq DESeq2
updated 12.0 years ago by 43k • written 12.0 years ago by ▴ 20
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2
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1.1k
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DESeq: normalizing additional sample to already normalized set of samples
Normalization edgeR DESeq Normalization edgeR DESeq
updated 12.0 years ago by 43k • written 12.0 years ago by ▴ 60
0
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2
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2.1k
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easyRNASeq for miRNA read counts
DESeq DESeq
updated 12.0 years ago by ▴ 320 • written 12.0 years ago by ★ 13k
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0
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1.3k
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DiffBind - Info
Normalization DESeq DiffBind Normalization DESeq DiffBind
12.0 years ago Rory Stark ★ 5.2k
0
votes
7
replies
3.5k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 12.0 years ago by ★ 1.2k • written 12.0 years ago by ★ 13k
1
vote
15
replies
4.9k
views
DEseq for chip-seq data normalisation
DESeq DESeq2 DESeq DESeq2
updated 12.0 years ago by ▴ 90 • written 12.1 years ago by ▴ 170
0
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3
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1.6k
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Deseq: Difference in number of reads
DESeq DESeq
updated 12.1 years ago by 43k • written 12.1 years ago by ▴ 20
0
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1
reply
690
views
RNA differential expression
DESeq DESeq
updated 12.1 years ago by 68k • written 12.1 years ago by ▴ 10
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4
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1.5k
views
DESeq: help with analysis
DESeq DESeq
updated 12.1 years ago by ▴ 140 • written 12.1 years ago by ▴ 190
0
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3
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2.2k
views
creating a newCountDataSet from HTSeq-count
DESeq DESeq
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ★ 1.5k
0
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2
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5.2k
views
Summarized Experiments - Combine
DESeq DESeq2 DESeq DESeq2
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 310
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0
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1.4k
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Measuring shifts in intronic expression independently of exons
GO DESeq DEXSeq ggbio GO DESeq DEXSeq ggbio
12.1 years ago James Perkins ▴ 60
0
votes
4
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1.9k
views
Measuring shifts in intronic expression independently of exons
GO DESeq DEXSeq ggbio GO DESeq DEXSeq ggbio
12.2 years ago James Perkins ▴ 60
0
votes
2
replies
1.4k
views
Unusual results with DESeq ?
miRNA Cancer DESeq miRNA Cancer DESeq
updated 12.2 years ago by ★ 3.8k • written 12.2 years ago by ▴ 40
0
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1
reply
1.6k
views
Question about Diffbind input control
Cancer DESeq DiffBind Cancer DESeq DiffBind
12.2 years ago Rory Stark ★ 5.2k
0
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0
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1.0k
views
Differential Expressed Genes analysis regarding limited genes
Sequencing Normalization GO DESeq Sequencing Normalization GO DESeq
12.2 years ago Michael Love 43k
0
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1
reply
812
views
Differential Expressed Genes analysis regarding limited genes
Sequencing DESeq Sequencing DESeq
updated 12.2 years ago by 43k • written 12.2 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Using the genes.count-tracking file from cuffdiff in DESeq
DESeq DESeq
updated 12.2 years ago by 43k • written 12.2 years ago by ★ 13k
0
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1
reply
875
views
DESeq query
GO DESeq GO DESeq
updated 12.3 years ago by 43k • written 12.3 years ago by ▴ 40
0
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3
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2.5k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
12.3 years ago Rory Stark ★ 5.2k
0
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6
replies
1.9k
views
request
RNASeq DESeq RNASeq DESeq
12.3 years ago Alexey Moskalev ▴ 30
0
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2
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1.2k
views
RNAseq data normalization without differential expression
RNASeq Normalization edgeR DESeq RNASeq Normalization edgeR DESeq
updated 12.3 years ago by 43k • written 12.3 years ago by ▴ 180
0
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1
reply
8.8k
views
Using DESeq normalized gene count to replace FPKM?
Visualization DESeq Visualization DESeq
updated 12.3 years ago by ★ 3.8k • written 12.3 years ago by ▴ 10
2
votes
4
replies
7.2k
views
Too many (?) differentially expressed genes - edgeR and DESeq
PROcess edgeR DESeq PROcess edgeR DESeq
updated 12.3 years ago by ★ 13k • written 12.3 years ago by ▴ 130
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2
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2.3k
views
DESeq. Error message on estimateDispersions blind
RNASeq DESeq RNASeq DESeq
updated 12.4 years ago by ★ 3.8k • written 12.4 years ago by ▴ 20
0
votes
4
replies
1.6k
views
DESeq2 design formula error?
DESeq DESeq2 DESeq DESeq2
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 140
0
votes
1
reply
1.3k
views
DESeq2 test over all timepoints?
edgeR DESeq DESeq2 edgeR DESeq DESeq2
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 140
0
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1
reply
4.0k
views
How to create a heatmap of a gene family (using subset of exprs(vsd) in DESeq)
DESeq DESeq
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ★ 13k
0
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1
reply
1.8k
views
RNA-seq: interaction effect with DESeq
DESeq DESeq
12.4 years ago galeb abu-ali ▴ 20
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0
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996
views
DEXSeq output table
DESeq DEXSeq DESeq DEXSeq
12.4 years ago Guest User ★ 13k
0
votes
2
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2.3k
views
Small RNA seq data analysis using DESeq
RNASeq DESeq RNASeq DESeq
updated 12.4 years ago by ★ 3.8k • written 12.4 years ago by ▴ 20
0
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1
reply
4.0k
views
TMM normalization of DESeq input data
Normalization edgeR DESeq Normalization edgeR DESeq
updated 12.4 years ago by ★ 7.9k • written 12.4 years ago by ★ 13k
0
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3
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1.2k
views
Question if DESeq can still be used after correction for T0?
DESeq DESeq
12.5 years ago Guest User ★ 13k
0
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0
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1.3k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq
12.5 years ago Gabriele Zoppoli ▴ 50
0
votes
10
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3.1k
views
DESeq /edgeR design problem for a small RNASeq
RNASeq edgeR DESeq RNASeq edgeR DESeq
updated 12.5 years ago by 53k • written 12.5 years ago by ▴ 90
0
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0
replies
1.2k
views
DEXSeq: PlotMA issues
graph DESeq DEXSeq graph DESeq DEXSeq
12.5 years ago Alejandro Reyes ★ 1.9k
0
votes
0
replies
1.9k
views
cpm on normalised counts (was "DESeq normalisation strategy")
Normalization edgeR DESeq Normalization edgeR DESeq
12.5 years ago Cittaro Davide ▴ 240
0
votes
5
replies
4.5k
views
[DESeq] p-value vs adjusted p-value
edgeR DESeq edgeR DESeq
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 20
0
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0
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2.3k
views
voom and RPKM for multi-species RNA-seq analysis
Genetics DESeq Genetics DESeq
12.5 years ago Julien Roux ▴ 90
0
votes
2
replies
2.2k
views
DESeq normalisation strategy
Normalization DESeq Normalization DESeq
updated 12.5 years ago by ★ 3.8k • written 12.5 years ago by ▴ 240
0
votes
3
replies
1.6k
views
DESeq2 - Different results between groups depending on which is first
DESeq DESeq
updated 12.5 years ago by 43k • written 12.5 years ago by ▴ 20
2
votes
1
reply
2.3k
views
DESeq Variance Stabilizing Transformation (now with non-embedded images)
Normalization Clustering DESeq DESeq2 Normalization Clustering DESeq DESeq2
updated 12.5 years ago by 43k • written 12.5 years ago by ▴ 50
0
votes
4
replies
2.7k
views
DESeq no recognizing row.names
DESeq DESeq
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 140
512 results • Page 6 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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