Showing : desEQ2 • reset
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DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
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5
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1.5k
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Mixed up sample info with plotPCA
plotMA ggplot2 plotPCA DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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4
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1.0k
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Extract LRT results for each comparison
LRT DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
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4
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1.6k
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.1 years ago Shihui • 0
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5
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1.1k
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DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.1 years ago Rockbar • 0
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3
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1000
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Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
2.1 years ago ruba-mahmoud • 0
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1.2k
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DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
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3
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2.5k
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How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.6 years ago by • 0
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4
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1.5k
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
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3
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1.5k
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Deseq2, enrichGO and ensembl ID
go DESeq2
updated 10 months ago by 68k • written 2.1 years ago by • 0
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3
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888
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
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3
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959
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The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.1 years ago by 68k • written 2.2 years ago by ▴ 10
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1
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1.6k
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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1
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843
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How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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7
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1.8k
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Permutation test in DESeq2?
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
3
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3
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1.1k
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EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.2 years ago Nisha • 0
3
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5
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2.2k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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585
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
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1
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675
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Unable to create ddf object
DESeqDataSetFromMatrix dds DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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2
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1.0k
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.2 years ago Beyza • 0
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3
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935
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Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 30
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2
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732
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Setting up a multi-factor experiement
DESeq2
2.2 years ago • updated 2.1 years ago jon50250 • 0
0
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848
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DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
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1
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1.2k
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results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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3
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1.5k
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DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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3
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1.3k
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
0
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1
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839
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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1.2k
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How to properly compare the group-specific samples using DEseq2
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
5
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13
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4.2k
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
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5
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1.6k
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How to use contrast with multiple treatments?
RNASeqdataanalysis DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
2
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2
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1.6k
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DESeq2 results - Annotating and exporting results
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
3
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7
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1.6k
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DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.2 years ago casco ▴ 10
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9
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1.7k
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DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.2 years ago mjd275 • 0
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8
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4.2k
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Significantly regulated genes produced by only a few affected samples
deseq2
written 7.7 years ago by ▴ 60
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12
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2.9k
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P-value inflation?
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
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2
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1.4k
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DESeq2 batch design
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.3 years ago by ▴ 10
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1
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1.1k
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Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
8
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15
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3.3k
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PCA percent variance DESeq2
PCA DESeq2
2.2 years ago IUH • 0
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6
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3.4k
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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916
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Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
0
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1
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627
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DEG by deseq2 by Race
DESeq2
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
0
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1
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732
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the confuse issue in DEseq2 among multi group
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
3
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2
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2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.2 years ago by ★ 4.1k • written 2.2 years ago by ▴ 10
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2
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1.8k
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
2.2 years ago Alessia ▴ 40
2
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5
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2.8k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
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1
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847
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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2
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715
views
No such file or directory DESeq2
rstudioScRNA DESeq2
written 2.3 years ago by • 0
2
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3
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3.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
0
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1
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991
views
DESeq2 interaction design
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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1
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2.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
4,836 results • Page 10 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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