Showing : DESEQ2 • reset
2
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3
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4.5k
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Change axis scale for plotting PCA in DESeq2
deseq2
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
2
votes
13
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2.1k
views
DESeq2 normalization resulting in very different Total read counts for samples
deseq2 normalization
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
1.2k
views
DESeq2 design formula
deseq2 design formula
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
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10
replies
4.1k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
votes
1
reply
910
views
LFC shrinkage Normal_vs_apeglm
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
1
vote
4
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1.0k
views
Design matrix design for the differentially expression analysis
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
2
replies
2.3k
views
How should I normalize my RNAseq data from Polysome profiling
deseq2 bioconductor RNAseq normalization Polysome_profiling
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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1
reply
1.6k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
481
views
Add basemean of "condition A" and "condition B" to the final table
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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1
reply
2.3k
views
DESeq2 plotCounts() function?
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
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2
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487
views
Raw RNAseq data upload in DEseq2
deseq2
5.8 years ago golam.mohiuddin • 0
6
votes
5
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4.1k
views
VST for scRNA-seq
deseq2 rnaseq normalization
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 50
1
vote
6
replies
2.0k
views
DESeq2 Normalisation out of excel data?
deseq2
5.8 years ago mueslirapper • 0
6
votes
13
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1.6k
views
DeSeq2 - adjusted p-value changes substantially after including non-coding RNA [SOLVED]
deseq2
5.8 years ago David Eccles (gringer) ▴ 30
0
votes
2
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1.3k
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
3
votes
5
replies
2.3k
views
How to extract DESeq2 results for an interaction design
deseq2 interaction
updated 5.8 years ago by ▴ 60 • written 5.8 years ago by • 0
11
votes
2
replies
6.4k
views
Filtering low variance genes for WGCNA
deseq2 WGCNA
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 40
0
votes
4
replies
1.2k
views
Normalizing for both gene size and library composition
RNA-seq normalization deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 40
0
votes
7
replies
1.9k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
5.8 years ago MANYA_BIOINFO • 0
1
vote
4
replies
1.3k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
3
replies
1.6k
views
Biplot environmental variables on top of PCA
deseq2 biplot plotpca
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 30
1
vote
4
replies
2.1k
views
install DESeq2 failed
deseq2
5.8 years ago petitechiarina • 0
0
votes
2
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644
views
Data normalization when genes have global alter
deseq2
written 5.8 years ago by • 0
4
votes
5
replies
974
views
apparent DESeq2::DESeq() performance decline since v1.22.2
DESeq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
2
replies
1.3k
views
Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2 rnaseq repeated measures time series design formula
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ★ 1.5k
1
vote
4
replies
925
views
Time series matrix design
deseq2
updated 5.8 years ago by 68k • written 5.9 years ago by ▴ 10
0
votes
9
replies
1.8k
views
DESeq2 model matrix question
deseq2
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
2
votes
2
replies
1.4k
views
Filtering in DESeq 2 basemean
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
1.7k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
5
replies
1.9k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.9 years ago omid.alamdari • 0
0
votes
1
reply
1.9k
views
plot statistic values in a DEseq2 plotCounts plot
deseq2 plotCounts pvalues RNAseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
2
replies
1.3k
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2 Paired Nested
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
2
replies
740
views
multiple group comparison
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
1
vote
7
replies
3.0k
views
DESeq2 namespace load failed for GenomeInfoDb
DESeq2
5.9 years ago Brian Smith ▴ 120
0
votes
4
replies
3.5k
views
How to install older version of DESeq2?
deseq2 software error
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
1
vote
1
reply
498
views
DESeq2: Less significant genes if more samples added?
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
2
replies
588
views
DESeq2 input data.
DESeq2 Normalization Input data
5.9 years ago Fischer-philipp ▴ 30
1
vote
2
replies
2.0k
views
Help understanding the contrast function in DESeq2
deseq2
5.9 years ago Eric de Sousa • 0
1
vote
3
replies
1.2k
views
typo in rnaseqGene workflow vignette.
rnaseqGene workflow deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
1
vote
1
reply
597
views
Siblings within but not across condition/treatment
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
8
replies
1.6k
views
DeSeq2: error in design individuals nested within groups
deseq2 methylation
5.9 years ago sara.blocquiaux • 0
1
vote
8
replies
2.0k
views
DESeq2 design matrix: covariates + nested replicates
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
6
replies
927
views
DESeq design matrix, control for contralateral hemisphere
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
2
votes
1
reply
1.9k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.9 years ago by ▴ 60 • written 5.9 years ago by ★ 1.5k
0
votes
2
replies
698
views
Sample Pairing Design Effects on Dispersion Estimates in DESeq2?
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
1.2k
views
Edit: How to analyze matched pairs RNA sequencing data over multiple time points using DESeq2?
deseq2 rnaseq ribotag trap
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
535
views
Sequencing machine as fixed effect in DEseq2?
deseq2 edger
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
votes
1
reply
740
views
Correlate DESeq2 variance stabilised counts with clinical covariates
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
1
vote
1
reply
634
views
DESeq2 Design - Within & Between Specimen Comparisons
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
4,839 results • Page 43 of 97
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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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