Showing : DESeq2 • reset
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RNA Seq using Lrt
DESeq2
7 months ago Rob • 0
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3
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1.0k
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Log2foldchange strange behavior
DESeq2
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
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1
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913
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WGCNA
WGCNA DESeq2
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
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1.1k
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 20
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1.3k
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PhD scholar
RNASeqAnalysis DESeq2
updated 8 months ago by 4.2k • written 8 months ago by • 0
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1
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493
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 8 months ago by 68k • written 8 months ago by ▴ 30
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3
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1.1k
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DESeq - help with pair wise comparisons
DESeq2
8 months ago bd2000 ▴ 30
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
8 months ago ktz • 0
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1
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771
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
4
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6
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1.6k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 8 months ago by ★ 5.0k • written 9 months ago by • 0
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4
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760
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
8 months ago Lennie • 0
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4
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1.2k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 8 months ago by • 0
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2
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1.2k
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
9 months ago • updated 6 months ago Erika • 0
1
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8
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2.7k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 months ago • updated 8 months ago Luca • 0
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2
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747
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 months ago by 43k • written 9 months ago by ▴ 20
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1
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465
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 9 months ago by 43k • written 9 months ago by • 0
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3
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993
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how many significant figures are there in DESeq2 output
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by ▴ 180
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5
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1.4k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
9 months ago picasa1983 • 0
3
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7
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2.4k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 9 months ago by ▴ 10 • written 6.8 years ago by ▴ 20
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1
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882
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 9 months ago by 68k • written 9 months ago by • 0
1
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657
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 10
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1
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453
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DEseq2 design for additive treatment
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
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2
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828
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Plot title for PCA in DESeq2
DESeq2
9 months ago AL • 0
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3
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1.0k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
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2
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1.4k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
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1
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415
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 months ago by 43k • written 10 months ago by • 0
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3
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832
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 months ago by • 0 • written 10 months ago by • 0
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2
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923
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 months ago by • 0 • written 10 months ago by • 0
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3
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615
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 9 months ago by • 0 • written 10 months ago by • 0
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3
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876
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 10 months ago by • 0 • written 10 months ago by ▴ 10
0
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1
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660
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
2
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2
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702
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
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4
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1.4k
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
10 months ago Quang NN ▴ 10
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2
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1.3k
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 months ago Blandine • 0
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5
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727
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
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4
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968
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 months ago Quang NN ▴ 10
2
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5
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816
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Differential variability modelling with vst() expression
limma DESeq2
written 11 months ago by • 0
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3
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924
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 11 months ago by • 0
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9
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1.7k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
11 months ago • updated 10 months ago Quang NN ▴ 10
1
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1
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900
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 11 months ago by 43k • written 11 months ago by • 0
0
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341
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
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1
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606
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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1
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731
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 months ago by 43k • written 11 months ago by • 0
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2
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717
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 months ago Kucsera • 0
1
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1
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553
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 11 months ago by 43k • written 12 months ago by • 0
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1.5k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 11 months ago by ▴ 40
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1.0k
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 11 months ago by ★ 5.0k • written 12 months ago by ▴ 10
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5
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1.0k
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Deseq2 Design
RNASeq DESeq2
updated 12 months ago by 68k • written 12 months ago by • 0
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5
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1.2k
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p value is 0, padj is 0
DESeq2
12 months ago Wirayatida • 0
1
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2
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
12 months ago georgii.vdovin • 0
4,841 results • Page 2 of 97
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Replies
Comment: p.adjust BH Question by TikTsoksocissalpc • 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
Awards • All
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