Showing : desEQ2 • reset
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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2
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469
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
11 months ago Anna • 0
1
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2
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787
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Deseq2 res Function
DESeq2
updated 11 months ago by 68k • written 11 months ago by ▴ 10
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4
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732
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
11 months ago NB • 0
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5
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754
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Identical samples after deseq2 batch effect removal
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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1
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564
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 11 months ago by 68k • written 11 months ago by • 0
1
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2
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482
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
11 months ago Denise • 0
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1
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405
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eRNAs count
RNASeq DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
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1
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613
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DESeq2 rerun returns different results
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
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511
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 11 months ago by 43k • written 12 months ago by • 0
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1
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567
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
2
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2
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1.0k
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Handling biological replicates in DESeq2
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.8 years ago by ▴ 30
1
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6
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1.6k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 months ago by 43k • written 12 months ago by ▴ 10
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2
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567
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 12 months ago by • 0
4
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5
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1.3k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
12 months ago LuciaNhu • 0
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1
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725
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Average expression of genes across replicates
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
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0
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402
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 months ago info ▴ 10
0
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11
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2.4k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 7 months ago by • 0 • written 12 months ago by • 0
0
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1
reply
555
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Deseq to output continous sequencing data
DESeq2
updated 12 months ago by 43k • written 13 months ago by • 0
1
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4
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1.3k
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Adjusted p-values become NA when sub-setting samples
DESeq2
13 months ago • updated 12 months ago txema.heredia • 0
3
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3
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1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 months ago by • 0
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2
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766
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 12 months ago by • 0
0
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1
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487
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
1
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4
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1.1k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
12 months ago boczniak767 ▴ 740
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1
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365
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
12 months ago JY • 0
0
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1
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462
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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2
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483
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how to extract expression matrix post deseq2
DESeq2
written 12 months ago by • 0
0
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2
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524
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Using Normalized Counts in DESeq2
DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
3
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2
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582
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When running contrasts, does it use normalized read counts?
DESeq2
13 months ago Katherine ▴ 20
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1
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409
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
3
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4
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1.2k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
13 months ago Eva ▴ 10
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4
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1.2k
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 12 months ago by ★ 5.0k • written 13 months ago by • 0
0
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1
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512
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
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4
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868
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
13 months ago jihoon.kim.1495 ▴ 10
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 months ago by 43k • written 13 months ago by • 0
5
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4
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979
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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2
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675
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
13 months ago paul.meraner • 0
0
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0
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586
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
13 months ago • updated 12 months ago info ▴ 10
1
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6
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1.4k
views
heatmap with batch effect
DESeq2 BatchEffect
written 13 months ago by • 0
0
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2
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729
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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 13 months ago by 43k • written 13 months ago by • 0
1
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1
reply
991
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 13 months ago by 68k • written 13 months ago by • 0
1
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1
reply
635
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
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1
reply
584
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
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2
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862
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
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2
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991
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
1
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2
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1.0k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 13 months ago by 43k • written 13 months ago by ▴ 10
1
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6
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1.7k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 12 months ago by ★ 5.0k • written 13 months ago by • 0
0
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1
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458
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
4,836 results • Page 3 of 97
Recent ...
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Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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