Showing : Deseq2 • reset
3
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4
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2.0k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.3 years ago Eva ▴ 10
2
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4
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1.3k
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DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
2.3 years ago Erika • 0
0
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1
reply
795
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Model matrix not full rank
DESeq2
2.3 years ago isabelle.dupanloup • 0
1
vote
2
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816
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Differential expression analysis with 7 factors (levels) at once?
DESeq2
2.3 years ago melander • 0
2
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2
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849
views
DESeq2: full model matrix is less than full rank
DESeq2
2.3 years ago melander • 0
0
votes
3
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4.0k
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
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4
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1.4k
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.3 years ago anne.hoffrichter • 0
0
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4
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1.1k
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Multi factor design and removing the effect of sex on main factor
DESeq2
2.3 years ago Mahendra • 0
0
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2
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3.1k
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
2.3 years ago Marina • 0
1
vote
3
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1.2k
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
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6
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2.0k
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Same few genes repeated in DESeq2 Results
DESeq2
2.3 years ago dsambo ▴ 10
0
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5
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1.4k
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DESeq2 analysis
DESe DESeq2
2.3 years ago Adèle • 0
4
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9
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3.6k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.3 years ago Luca • 0
0
votes
1
reply
698
views
Using DEseq2 for two conditions with different dispersions
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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0
replies
822
views
Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
CLANG DESeq2
2.3 years ago lokapal • 0
1
vote
2
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890
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
8
replies
1.4k
views
Deseq2 Results are different using batch design
DESeq2
2.3 years ago hemantcnaik • 0
1
vote
2
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814
views
Building Multifactor Model in DESeq2
DESeq2
2.3 years ago Abhishek Singh ▴ 20
0
votes
11
replies
3.1k
views
Unable to install DESeq2
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.3 years ago Matteo • 0
0
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2
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1.8k
views
Creating heatmaps with 2 Log Fold Changes in DESEQ2
DESeq2
written 2.3 years ago by • 0
0
votes
1
reply
595
views
Tximport - Is transcript level expression sum equal to summarisetogene() results
tximpor DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
vote
2
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906
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
2.3 years ago Bushra • 0
0
votes
4
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1.3k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 20
0
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1
reply
1.2k
views
Specifying design in DESeqDataSetFromMatrix
DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
1
vote
1
reply
1.6k
views
DESeq2 LRT Reduced Formula
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
551
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
9
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1.5k
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
3
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902
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p-value<0.05 for a gene with zero counts?
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 20
2
votes
1
reply
714
views
Running DEseq2 without "factor" gives unexpected results
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
1
reply
1.3k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 16 months ago by 43k • written 2.3 years ago by • 0
4
votes
5
replies
3.8k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
7
votes
3
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1.7k
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by ▴ 20
0
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3
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1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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1
reply
952
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
8
votes
7
replies
3.1k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.4 years ago by ▴ 20 • written 3.1 years ago by ▴ 20
1
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8
replies
2.6k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 19 months ago by ★ 13k • written 2.4 years ago by ▴ 10
2
votes
9
replies
2.4k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.4 years ago • updated 2.3 years ago Ndimensional ▴ 20
2
votes
3
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1.9k
views
Identify highly variable genes after vst
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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5
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1.9k
views
DESeq2 design formula
designformula DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
0
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1
reply
1.2k
views
really low padj value from DESeq2
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
1
reply
999
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
0
votes
2
replies
902
views
plotCounts label each sample
p DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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2
replies
1.3k
views
Heat Map
ColData pheatmap DESeq2
written 2.4 years ago by • 0
1
vote
6
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3.2k
views
Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
3
replies
1.1k
views
Normalization of different input materials
Normalization DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
3
votes
2
replies
1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 30
2
votes
8
replies
3.2k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 2.4 years ago by ▴ 10
0
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9
replies
2.7k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
votes
3
replies
1.4k
views
DESeq2 with nbinomGLM issues
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
4,836 results • Page 11 of 97
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
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…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
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