Showing : DESEq2 • reset
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.1 years ago m.glymenaki • 0
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4
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1.3k
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DESeq2 with multiple variable give me different results
Factor Levels Dispersionestimates DESeq2
4.1 years ago rafaelsolersanblas ▴ 50
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2
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1.2k
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DESeq2 ratio of ratios and p-value
DESeq2 dese
4.1 years ago wilfried.guiblet • 0
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8
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1.9k
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DESeq2 cannot relevel
DESeq2
4.1 years ago Jorge • 0
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5
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2.0k
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DESeq2: error while ploting figure
R DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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DeSeq2 Comparing One group vs Two groups
DESeq2
written 4.1 years ago by ▴ 10
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6
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2.3k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
4.1 years ago ary.lech ▴ 10
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2.3k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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4
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2.1k
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DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2 limma modelmatrix edgeR designmatrix
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
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lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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659
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Interaction model genes don't intersect
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
3
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Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
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2
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1.5k
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DESeq2 normalization when using with derfinder
Normalization DESeq2 derfinder
4.1 years ago Debayan ▴ 20
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1.7k
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Correct workflow for analyzing differentially expressed genes and correlation analyses on TCGA data?
DESeq2
4.1 years ago mario.keller.1988 ▴ 20
4
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1
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3.1k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
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Error in designing DESeq2 time pointed experiments
LTR DESeq2
4.1 years ago AZ ▴ 30
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2
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1.2k
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results() function and finding the difference of differences
interactions DESeq2
4.1 years ago Nayrouz • 0
1
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1
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972
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DESEQ2 when global gene expression changes exist
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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1.7k
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DESeq2 PlotCounts() function
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix deseq2 DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by • 0
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Interpretation of Log 2 fold change
DESeq2
4.1 years ago adeler001 • 0
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Installing DESEq2 Error: unable to access index for repository https://bioconductor.org
Install Bioconductor DESeq2
4.1 years ago ladypurrsia ▴ 10
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3.2k
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DESeq2 version
DESeq2
4.1 years ago adeler001 • 0
2
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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How to analyze 10 samples (5 control, 5 treatment) which perform the experiment from different day
DESeq2 RNASeq
4.1 years ago Yosapol • 0
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6
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2.2k
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DESeq2 Normalization
DESeq2
4.1 years ago Jamie • 0
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2
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1.3k
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DESeq function stuck on estimating gene-wise dispersion.
DESeq2
4.1 years ago m.deluca • 0
1
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832
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Multiple samples per individual
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 50
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2.5k
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Model matrix not full rank, then
DESeq2
4.1 years ago Sonia • 0
2
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1
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2.6k
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How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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1.7k
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small log2foldChange value in the most significant genes
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 30
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.1 years ago • updated 2.5 years ago diangomaiga • 0
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952
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where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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Is it advisable to input a count matrix that consists of reads aligned using different algorithms (HT-Seq and Salmon)?
DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by • 0
0
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.1 years ago p.l.chen • 0
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5
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6.9k
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using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.3 years ago by ▴ 20 • written 4.1 years ago by ▴ 20
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2
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1.1k
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Extracting the LFC from a reduced model
DESeq2
4.2 years ago • updated 4.1 years ago Sonia • 0
2
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2
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9.1k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by ▴ 10
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DESeq2 differential expression analysis of protein coding genes only
DESeq2
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
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DESeq2 design formula
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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4.5k
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DESeq2 error in design~ code
DESeq2
4.2 years ago • updated 4.1 years ago Abdou-samad • 0
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8
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2.2k
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Three conditions and two time points
DifferentialExpression DESeq2 time
4.2 years ago • updated 4.1 years ago AZ ▴ 30
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4
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4.8k
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Question on the fold change estimate
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
2
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4
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1.5k
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Remove genes in a list from cts
DESeq2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by ▴ 50
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5
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DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
4.2 years ago Sonia • 0
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4
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6.0k
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Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.2 years ago Sandhiya • 0
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6
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2.6k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
4.2 years ago s-rhussien • 0
3
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4
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1.6k
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Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
4.2 years ago Rui ▴ 10
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2.7k
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Nested, multifactorial design formular for targeted contrast of a factor interaction
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
4,840 results • Page 26 of 97
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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