Showing : DifferentialExpression • reset
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.6 years ago sreeshmaraj72 • 0
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.3 years ago by • 0 • written 4.6 years ago by ▴ 20
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 22 months ago by ★ 5.0k • written 3.8 years ago by ▴ 70
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
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10
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.1 years ago Hajar • 0
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7
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Which Limma guide is recommended ?
limma R DifferentialExpression
3.7 years ago • updated 3.6 years ago JAcky • 0
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3.1k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.6 years ago Jane ▴ 10
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3
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990
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 15 months ago by 53k • written 16 months ago by • 0
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 24 days ago by • 0
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9
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2.4k
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 840
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 18 months ago by • 0 • written 21 months ago by ▴ 60
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1.6k
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 16 months ago by • 0
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3
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1.6k
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.8 years ago nhaus ▴ 70
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2
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1.4k
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
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8
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3.3k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 2.5 years ago by ▴ 10
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 24 months ago by • 0
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3
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differential gene expression
limma differentialexpression
updated 11.2 years ago by ▴ 760 • written 11.2 years ago by ▴ 20
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11
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.8 years ago mohammedtoufiq91 ▴ 10
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2
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891
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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6
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2.2k
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.1 years ago by • 0
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5
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How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
4.3 years ago zhxiaokang ▴ 20
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2
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1.5k
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
5
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2
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3.6k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.3 years ago by 53k • written 4.3 years ago by ▴ 10
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2
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2.5k
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Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 30
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3
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Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
11.2 years ago • updated 11.1 years ago asaferali • 0
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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5
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 13 months ago by 53k • written 21 months ago by ▴ 60
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.7 years ago by ▴ 10 • written 11.7 years ago by 53k
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998
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Wald or LR Test
DESeq2 DifferentialExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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3
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2.2k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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7
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4.7k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 20
3
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7
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2.0k
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Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 30
4
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2
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7.4k
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DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 11.2 years ago by 43k • written 11.2 years ago by ▴ 110
2
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4
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1.4k
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Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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637
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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1.0k
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 30
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.8 years ago by ★ 29k • written 4.8 years ago by • 0
3
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6
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do I have to do this step in creating DGEList ?
DifferentialExpression
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
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882
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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1
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862
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Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.8 years ago by 43k • written 4.9 years ago by • 0
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3
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2.1k
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Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
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5
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1.1k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 16 months ago by 68k • written 17 months ago by • 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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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.7 years ago • updated 3.6 years ago Ismail • 0
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2
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1.0k
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DESeq2 with very large feature set
DESeq2 DifferentialExpression
5.1 years ago ramiro.barrantes ▴ 10
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1.1k
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Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.7 years ago AZ ▴ 30
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Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
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
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