Showing : DESEQ2 • reset
0
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8
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DESeq2: Variable Importance
DESeq2 RNASeq
updated 2 days ago by 33k • written 3 days ago by • 0
0
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3
replies
112
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matrix with Salmon gene-level quantifications in DESeq
DESeq2
updated 1 day ago by 33k • written 3 days ago by ▴ 10
0
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1
reply
69
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DESeq2 - how to account for patient, batch and condition
DESeq2
updated 4 days ago by 57k • written 5 days ago by • 0
2
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3
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86
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2 days ago by • 0 • written 5 days ago by • 0
0
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9
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198
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Why is my plot count does not fit with log fold change result?
DESeq2
updated 5 days ago by 33k • written 6 days ago by ▴ 30
0
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4
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96
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Number of genes differs between two design formulas in deseq2
DESeq2
6 days ago Mohamed Malek • 0
1
vote
6
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161
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Statistics on normalized counts
DESeq2
updated 6 days ago by • 0 • written 6 days ago by • 0
0
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3
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104
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[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 6 days ago by 33k • written 7 days ago by ▴ 10
1
vote
1
reply
79
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DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 7 days ago by 33k • written 9 days ago by • 0
0
votes
1
reply
78
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Why is the number of DEG different when comparing A versus B and B versus A?
DESeq2
updated 7 days ago by 33k • written 7 days ago by • 0
0
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2
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156
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where to download practice data
DESeq2
updated 10 days ago by ▴ 640 • written 12 days ago by • 0
0
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1
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78
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DESeq2: Paired samples (before and after treatment) with different responses
DESeq2
updated 11 days ago by ▴ 770 • written 11 days ago by • 0
2
votes
2
replies
121
views
How to remove batch effect from multiple rna-seq dataset before running deseq2
DESeq2
11 days ago • updated 10 days ago Yosapol • 0
0
votes
1
reply
93
views
Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
12 days ago • updated 11 days ago Serge • 0
0
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3
replies
115
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 11 days ago by ▴ 770 • written 12 days ago by • 0
1
vote
1
reply
88
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[DESeq2] - Making DESeq Dataset object from csv of already normalized counts.
DESeq2
12 days ago Michael • 0
0
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2
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99
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DESeq2 - Cannot replicate log2FC calculations
DESeq2
13 days ago Sara • 0
0
votes
2
replies
101
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DESeq2 time-series with two conditions and several patients
DESeq2
15 days ago • updated 5 days ago Karolina Trachtova • 0
1
vote
2
replies
119
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Design Formula, PCA, and Sex Effect
DESeq2
16 days ago • updated 15 days ago GHI ▴ 10
0
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1
reply
75
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DESeq2 "not full rank" with design design ~Gender+ Age
DESeq DESeq2
updated 17 days ago by ▴ 770 • written 17 days ago by • 0
4
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2
replies
5.5k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 2.4 years ago by ▴ 20
0
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3
replies
110
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Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 6 days ago by 33k • written 18 days ago by • 0
4
votes
3
replies
132
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 18 days ago by 33k • written 19 days ago by ▴ 30
0
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1
reply
66
views
FDR Correction
dada2 Metagenomics DESeq2
updated 19 days ago by 33k • written 19 days ago by • 0
2
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8
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209
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
26 days ago • updated 18 days ago Jane • 0
6
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12
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252
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ColData use only certain variable within
DESeq2
19 days ago Bine ▴ 10
0
votes
1
reply
74
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 20 days ago by 33k • written 20 days ago by • 0
1
vote
2
replies
121
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Plotting FPKM
ggplots2 DESeq2 fpkm()
20 days ago • updated 15 days ago Gime ▴ 10
1
vote
4
replies
113
views
Incorrect 2-fold change reported in DESeq2 Data
DESeq2
20 days ago • updated 19 days ago Naphtap92 ▴ 10
0
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3
replies
88
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Can't install DESeq2 because of libxml
deseq2 libxml xml
updated 20 days ago by 33k • written 20 days ago by • 0
4
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14
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1.9k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 23 days ago by 33k • written 22 months ago by • 0
0
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3
replies
125
views
It takes a so long time to run DESeq2 on 1000 samples
DESeq2
updated 23 days ago by 33k • written 24 days ago by • 0
0
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1
reply
108
views
DESeq2 design help
DESeq2
updated 24 days ago by 33k • written 24 days ago by • 0
0
votes
4
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113
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Inflation of zero or low counts in one condition - is DESeq2 with ZINB-WaVE an appropriate tool for such data?
DESeq2
25 days ago • updated 22 days ago miyakokodama • 0
0
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1
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93
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 25 days ago by 33k • written 25 days ago by • 0
2
votes
1
reply
124
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Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 26 days ago by 33k • written 4 weeks ago by • 0
1
vote
2
replies
106
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Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
27 days ago • updated 26 days ago fernandogs97 • 0
0
votes
1
reply
92
views
Dispersion Factors Not Being Calculated For Every Gene
DESeq2
updated 26 days ago by 33k • written 27 days ago by • 0
0
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4
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117
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
28 days ago jehimi • 0
0
votes
1
reply
93
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 28 days ago by 33k • written 28 days ago by • 0
0
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2
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114
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Technical reps
RNASeq DESeq2
updated 27 days ago by ▴ 640 • written 28 days ago by • 0
4
votes
7
replies
198
views
Controlling for Batch Effect and Grouping in DESEQ2
DESeq2
updated 28 days ago by 33k • written 4 weeks ago by ▴ 10
0
votes
4
replies
263
views
Problems installing DESeq2
DESeq2
4 weeks ago • updated 29 days ago kvitt_silver • 0
1
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2
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109
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Grouping DESEQ2 with additional variable
DESeq2
4 weeks ago Bine ▴ 10
2
votes
2
replies
107
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
4 weeks ago tjbencomo • 0
0
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1
reply
78
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DeSeq2 with 2 conditions and 3 time points
deseq2 timepoints
updated 4 weeks ago by ▴ 770 • written 4 weeks ago by • 0
2
votes
11
replies
213
views
phenotypic table for DESeqDataSetFromHTSeqCount
DESeq2
4 weeks ago • updated 28 days ago rbenel ▴ 20
2
votes
2
replies
115
views
DESEQ2 colData object
DESeq2
4 weeks ago Bine ▴ 10
4
votes
3
replies
154
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 4 weeks ago by ★ 26k • written 4 weeks ago by ▴ 20
2
votes
6
replies
181
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DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
5 weeks ago Saulius • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: New annotation package - no response from packages@bioconductor.org by shepherl 2.7k
I would make sure you are registered and are following the name of the package as a watched tag here on the support site so that if questio…
Comment: New annotation package - no response from packages@bioconductor.org by athief ▴ 10
Thanks for the update. Anything I shall do/prepare in the meantime?
Comment: New annotation package - no response from packages@bioconductor.org by shepherl 2.7k
As an update. We are still working on branching annotations from the recent Bioconductor release. We should have this available within the…
Comment: installing older versions of packages by zuljiamel1991 • 0
That works when specific Bioconductor version is needed. However, within the same version of Bioconductor, few versions of packages are rel…
Comment: installing older versions of packages by zuljiamel1991 • 0
I will check this one, thank you!
Votes
Comment: New annotation package - no response from packages@bioconductor.org
Comment: How to do annotation with Limma
Answer: No counts, just fold change data
How to select summit size for histone ChiP-Seq in Diffbind
A: How to select summit size for histone ChiP-Seq in Diffbind
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