Showing : DESeq2 • reset
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
2
votes
4
replies
1.1k
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
16 months ago jihoon.kim.1495 ▴ 10
0
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 16 months ago by 43k • written 16 months ago by • 0
5
votes
4
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1.2k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 16 months ago by ★ 5.0k • written 17 months ago by • 0
0
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2
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774
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
17 months ago • updated 16 months ago paul.meraner • 0
0
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0
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714
views
News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
17 months ago • updated 16 months ago info ▴ 10
1
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6
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1.6k
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heatmap with batch effect
DESeq2 BatchEffect
written 17 months ago by • 0
0
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2
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840
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
1
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1
reply
1.4k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
1
reply
790
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
1
vote
1
reply
634
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
1
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2
replies
1.0k
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 17 months ago by 43k • written 17 months ago by ▴ 10
0
votes
2
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1.1k
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
1
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2
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1.1k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 17 months ago by 43k • written 17 months ago by ▴ 10
1
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6
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2.4k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 16 months ago by ★ 5.0k • written 17 months ago by • 0
0
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1
reply
519
views
Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
17
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9
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8.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 17 months ago by 68k • written 9.7 years ago by ▴ 10
0
votes
1
reply
754
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
2
replies
955
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 17 months ago by ★ 1.4k • written 18 months ago by • 0
0
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5
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2.4k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.8 years ago by • 0
3
votes
6
replies
2.1k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 17 months ago by 43k • written 18 months ago by • 0
3
votes
6
replies
33k
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Deseq: What does "BaseMean" mean?
deseq2
written 7.4 years ago by • 0
0
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2
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2.0k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
4
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11
replies
2.0k
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
18 months ago boczniak767 ▴ 740
3
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4
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939
views
Gene filtering in DESeq2
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
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2
replies
937
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 18 months ago by • 0
1
vote
2
replies
543
views
Deseq2 - differenc in results
DESeq2
written 18 months ago by • 0
0
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7
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1.2k
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DESeq design with and without intercept is giving different results
DESeq2
written 18 months ago by • 0
1
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5
replies
1.8k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 18 months ago by 53k • written 18 months ago by • 0
0
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3
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1.3k
views
More significant genes after lfcShrink in DEseq2?
DESeq2
written 18 months ago by • 0
0
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3
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1.1k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 18 months ago by 53k • written 18 months ago by • 0
0
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2
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764
views
Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 18 months ago by • 0
6
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5
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5.1k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 13 months ago by ▴ 20 • written 18 months ago by • 0
3
votes
3
replies
1.9k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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2
replies
1.3k
views
R is Removing the Gene Names in My Count Data
DESeq2
updated 18 months ago by ▴ 70 • written 18 months ago by • 0
1
vote
4
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1.7k
views
Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
18 months ago Bob ▴ 30
0
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1
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670
views
Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
3
replies
1.3k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 18 months ago by • 0
3
votes
5
replies
2.9k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
2
votes
1
reply
2.0k
views
DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
votes
2
replies
970
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
18 months ago BioinfGuru ▴ 70
1
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2
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855
views
Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
19 months ago • updated 18 months ago DL • 0
0
votes
3
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1.1k
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 18 months ago by 68k • written 19 months ago by • 0
6
votes
15
replies
2.8k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 18 months ago by ★ 1.4k • written 19 months ago by • 0
1
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2
replies
1.5k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
19 months ago grothmn • 0
0
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1
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1.6k
views
HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 19 months ago by 68k • written 19 months ago by • 0
4
votes
7
replies
2.9k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 19 months ago by ▴ 10 • written 20 months ago by ▴ 70
0
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1
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972
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
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1.1k
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 19 months ago by 43k • written 19 months ago by • 0
2
votes
3
replies
1.1k
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 2.1 years ago by • 0
4,851 results • Page 4 of 98
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Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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