Showing : DESEQ2 • reset
6
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3
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8.3k
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DESeq2 GLM modelling and Wald's test
deseq2
updated 6.4 years ago by ▴ 40 • written 6.4 years ago by ▴ 10
4
votes
4
replies
2.0k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 40
2
votes
2
replies
770
views
DESeq2 positive results for genes with high samples counts dispersion
DESeq2
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2 design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
votes
2
replies
1.2k
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
2
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3
replies
26k
views
Contrast for DESeq2 design with interaction and blocking factor
deseq2
6.5 years ago • updated 6.4 years ago erwan.scaon ▴ 10
0
votes
3
replies
2.0k
views
ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
6.5 years ago sebastian.lobentanzer ▴ 60
2
votes
8
replies
4.3k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
4
votes
16
replies
7.3k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
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1
reply
780
views
Differential abundance analysis of 16S data with extremely unbalanced cohorts in Deseq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
742
views
How can I import KEGG annotations
deseq2 annotation
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
2
votes
1
reply
662
views
Does response on subset of data in DESeq
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ★ 1.4k
0
votes
2
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4.2k
views
Intercept result in DESeq2 two factor model
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
0
votes
1
reply
560
views
Package for RNA-Chromatin Interaction Matrix for Differential Gene Feature Calling?
Differential Peak Calling DiffBind DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
1
reply
616
views
DESeq2 for comparisons within group
deseq2 interaction factors complex design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
860
views
Using already normalized counts
deseq2
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
2
votes
6
replies
1.5k
views
DESeq2 analysis of no-normalized data yielded biased results
deseq2 normalization
6.5 years ago Victor Chano • 0
0
votes
6
replies
2.1k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
10
votes
20
replies
26k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 13 months ago by 68k • written 6.5 years ago by ▴ 30
0
votes
3
replies
886
views
Salmon / tximport
tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
3
votes
3
replies
2.1k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
1
reply
1.3k
views
Multiple groups and two methods to analyse them with DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
0
votes
1
reply
1.4k
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
5
votes
5
replies
3.1k
views
Principal components in DESeq2
deseq2
6.5 years ago Mozart ▴ 30
1
vote
3
replies
1.6k
views
DESeq2 gives weird results
deseq2 salmon
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
6
replies
1.8k
views
dseq2 results synergy contrast
deseq2 contrast synergy
updated 2.4 years ago by ▴ 10 • written 6.5 years ago by ▴ 90
0
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1
reply
974
views
Error with DESeq2 about integer number
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
reply
648
views
Questions about DESeq2 functionalities from beginners
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
3
replies
1.1k
views
Shrinkage and gene ranking
deseq2
updated 3.6 years ago by 43k • written 6.5 years ago by • 0
1
vote
11
replies
1.2k
views
Design formula DESeq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
1
reply
2.1k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
2
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2
replies
1.2k
views
DESeq2 for differential expression between species
deseq2 rna-seq
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
1.0k
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
1
reply
2.5k
views
Not integers values
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
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4
replies
1.1k
views
How to subset data
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
0
votes
1
reply
586
views
DESeq2 Multi-Factor anlaysis
deseq2 multi-factor
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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3
replies
1.4k
views
Is Background Correction necessary before DESeq analysis
deseq2 cancer
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
5
replies
1.5k
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
vote
4
replies
1.4k
views
DESeq2:Why is there an oblique line in my MA picture, which happened before, what caused this?
deseq2 cancer
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
8
replies
1.7k
views
Custom post-normalization counts from DESeq2
DEG deseq2 Covariate
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
4
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1
reply
1.5k
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 20
0
votes
1
reply
796
views
Phylpseq to deseq2
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
2
votes
5
replies
3.1k
views
DESeq2 complex model matrix and result interpretations
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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4
replies
1.4k
views
DESeQ2 design multiple conditions
deseq2
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
2
votes
4
replies
2.8k
views
How to get the regression slope coefficient from DESeq2 analysis of continuous data
deseq2
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
6
replies
2.3k
views
Plot genes with similar expression patterns
deseq2 R RNASeq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
3
votes
1
reply
2.4k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
0
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3
replies
2.5k
views
Problem constructing DESeq objects with large integers.
deseq2 recount
6.5 years ago Zach Brehm • 0
2
votes
1
reply
2.7k
views
Understanding Likelihood ratio test
deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.0k
views
Differential expression between groups with zero counts in DESEQ2
zero counts deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
4,839 results • Page 50 of 97
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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