Showing : deseq • reset
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DESeq nbinomGLMTest specific comparisons
DESeq DESeq2 DESeq DESeq2
updated 11.7 years ago by ★ 7.9k • written 11.7 years ago by ▴ 40
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diffbind question : bSubControl with DEseq
DESeq DiffBind DESeq DiffBind
11.7 years ago Rory Stark ★ 5.2k
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1
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627
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Using DESeq to test for null ratios other than 1:1
DESeq DESeq
updated 11.8 years ago by ★ 3.8k • written 11.8 years ago by ★ 13k
0
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1
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837
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DESeq problem
DESeq DESeq
updated 11.8 years ago by ▴ 540 • written 11.8 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 11.8 years ago by ▴ 320 • written 11.8 years ago by 53k
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0
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1.4k
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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
11.8 years ago Nicolas Delhomme ▴ 320
0
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1
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799
views
DESeq nbinomGLMTest specific comparisons
DESeq DESeq
updated 11.9 years ago by ★ 13k • written 11.9 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 11.9 years ago by 43k • written 11.9 years ago by ▴ 20
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2
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1.0k
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DESeq: normalizing additional sample to already normalized set of samples
Normalization edgeR DESeq Normalization edgeR DESeq
updated 11.9 years ago by 43k • written 11.9 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 11.9 years ago by ▴ 320 • written 11.9 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
11.9 years ago Rory Stark ★ 5.2k
0
votes
7
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3.4k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 11.9 years ago by ★ 1.2k • written 11.9 years ago by ★ 13k
1
vote
15
replies
4.8k
views
DEseq for chip-seq data normalisation
DESeq DESeq2 DESeq DESeq2
updated 11.9 years ago by ▴ 90 • written 11.9 years ago by ▴ 170
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3
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1.5k
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Deseq: Difference in number of reads
DESeq DESeq
updated 12.0 years ago by 43k • written 12.0 years ago by ▴ 20
0
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1
reply
674
views
RNA differential expression
DESeq DESeq
updated 12.0 years ago by 68k • written 12.0 years ago by ▴ 10
0
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4
replies
1.5k
views
DESeq: help with analysis
DESeq DESeq
updated 12.0 years ago by ▴ 140 • written 12.0 years ago by ▴ 190
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3
replies
2.2k
views
creating a newCountDataSet from HTSeq-count
DESeq DESeq
updated 12.0 years ago by ★ 13k • written 12.0 years ago by ★ 1.5k
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2
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5.2k
views
Summarized Experiments - Combine
DESeq DESeq2 DESeq DESeq2
updated 12.0 years ago by ★ 6.8k • written 12.0 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
12.0 years ago James Perkins ▴ 60
0
votes
4
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1.8k
views
Measuring shifts in intronic expression independently of exons
GO DESeq DEXSeq ggbio GO DESeq DEXSeq ggbio
12.0 years ago James Perkins ▴ 60
0
votes
2
replies
1.4k
views
Unusual results with DESeq ?
miRNA Cancer DESeq miRNA Cancer DESeq
updated 12.1 years ago by ★ 3.8k • written 12.1 years ago by ▴ 40
0
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1
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1.6k
views
Question about Diffbind input control
Cancer DESeq DiffBind Cancer DESeq DiffBind
12.1 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
12.1 years ago Michael Love 43k
0
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1
reply
798
views
Differential Expressed Genes analysis regarding limited genes
Sequencing DESeq Sequencing DESeq
updated 12.1 years ago by 43k • written 12.1 years ago by ▴ 10
0
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1
reply
1.7k
views
Using the genes.count-tracking file from cuffdiff in DESeq
DESeq DESeq
updated 12.1 years ago by 43k • written 12.1 years ago by ★ 13k
0
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1
reply
851
views
DESeq query
GO DESeq GO DESeq
updated 12.1 years ago by 43k • written 12.1 years ago by ▴ 40
0
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3
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2.4k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
12.1 years ago Rory Stark ★ 5.2k
0
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6
replies
1.9k
views
request
RNASeq DESeq RNASeq DESeq
12.2 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 12.2 years ago by 43k • written 12.2 years ago by ▴ 180
0
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1
reply
8.7k
views
Using DESeq normalized gene count to replace FPKM?
Visualization DESeq Visualization DESeq
updated 12.2 years ago by ★ 3.8k • written 12.2 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 12.2 years ago by ★ 13k • written 12.2 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 12.2 years ago by ★ 3.8k • written 12.2 years ago by ▴ 20
0
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4
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1.5k
views
DESeq2 design formula error?
DESeq DESeq2 DESeq DESeq2
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ▴ 140
0
votes
1
reply
1.3k
views
DESeq2 test over all timepoints?
edgeR DESeq DESeq2 edgeR DESeq DESeq2
updated 12.2 years ago by 43k • written 12.2 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 12.3 years ago by ★ 13k • written 12.3 years ago by ★ 13k
0
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1
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1.8k
views
RNA-seq: interaction effect with DESeq
DESeq DESeq
12.3 years ago galeb abu-ali ▴ 20
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0
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964
views
DEXSeq output table
DESeq DEXSeq DESeq DEXSeq
12.3 years ago Guest User ★ 13k
0
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2
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2.2k
views
Small RNA seq data analysis using DESeq
RNASeq DESeq RNASeq DESeq
updated 12.3 years ago by ★ 3.8k • written 12.3 years ago by ▴ 20
0
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1
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3.9k
views
TMM normalization of DESeq input data
Normalization edgeR DESeq Normalization edgeR DESeq
updated 12.3 years ago by ★ 7.9k • written 12.3 years ago by ★ 13k
0
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3
replies
1.1k
views
Question if DESeq can still be used after correction for T0?
DESeq DESeq
12.3 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
12.3 years ago Gabriele Zoppoli ▴ 50
0
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10
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3.0k
views
DESeq /edgeR design problem for a small RNASeq
RNASeq edgeR DESeq RNASeq edgeR DESeq
updated 12.3 years ago by 53k • written 12.3 years ago by ▴ 90
0
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0
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1.2k
views
DEXSeq: PlotMA issues
graph DESeq DEXSeq graph DESeq DEXSeq
12.3 years ago Alejandro Reyes ★ 1.9k
0
votes
0
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1.9k
views
cpm on normalised counts (was "DESeq normalisation strategy")
Normalization edgeR DESeq Normalization edgeR DESeq
12.3 years ago Cittaro Davide ▴ 240
0
votes
5
replies
4.4k
views
[DESeq] p-value vs adjusted p-value
edgeR DESeq edgeR DESeq
updated 12.3 years ago by ★ 13k • written 12.3 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
12.3 years ago Julien Roux ▴ 90
0
votes
2
replies
2.2k
views
DESeq normalisation strategy
Normalization DESeq Normalization DESeq
updated 12.4 years ago by ★ 3.8k • written 12.4 years ago by ▴ 240
0
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3
replies
1.5k
views
DESeq2 - Different results between groups depending on which is first
DESeq DESeq
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 20
2
votes
1
reply
2.2k
views
DESeq Variance Stabilizing Transformation (now with non-embedded images)
Normalization Clustering DESeq DESeq2 Normalization Clustering DESeq DESeq2
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 50
0
votes
4
replies
2.7k
views
DESeq no recognizing row.names
DESeq DESeq
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 140
512 results • Page 6 of 11
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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…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
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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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