Showing : differentialexpression • reset
3
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 25 days ago by • 0
2
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2
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264
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
27 days ago • updated 26 days ago jamie.gearing ▴ 60
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4
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213
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
4 weeks ago • updated 28 days ago Denise • 0
0
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1
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589
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 7 months ago by • 0
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1
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1.3k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
1
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
8 months ago ktz • 0
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
0
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1
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417
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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
0
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1
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663
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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
0
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5
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734
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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
0
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2
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725
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
12 months ago Tadeoye ▴ 20
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1.8k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 months ago by 68k • written 12 months ago by • 0
3
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3
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950
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 12 months ago by 53k • written 13 months ago by • 0
1
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3
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888
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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5
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1.2k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
0
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1
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540
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 14 months ago by • 0
0
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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 16 months ago by 53k • written 16 months ago by • 0
3
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3
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1.7k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 16 months ago by 68k • written 16 months ago by • 0
0
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3
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1.0k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 16 months ago by • 0
3
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5
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2.3k
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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
0
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3
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1.0k
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
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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 17 months ago by 68k • written 17 months ago by • 0
0
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0
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813
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
17 months ago nhaus ▴ 70
3
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5
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3.4k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 18 months ago by • 0 • written 21 months ago by ▴ 60
2
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1
reply
834
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by ▴ 70
0
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4
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1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 months ago vohara4 • 0
0
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1
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651
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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3
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800
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by • 0
1
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3
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1.1k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 19 months ago by 53k • written 19 months ago by • 0
0
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1
reply
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
2
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7
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2.0k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
19 months ago sajadahmad41454 • 0
0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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3
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934
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
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2
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832
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by ▴ 70
5
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6
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1.5k
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by ▴ 70
1
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3
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936
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
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2
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1.0k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
1
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2
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899
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
21 months ago • updated 20 months ago Chanderkant Chaudhary • 0
8
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5
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3.3k
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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
0
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2
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893
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
0
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2
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1.2k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
1
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3
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1.1k
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
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4
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1.1k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
21 months ago mperalc • 0
0
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0
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773
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
2
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1
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807
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
3
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2
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1.1k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
22 months ago Shaimaa Gamal • 0
4
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3
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1.2k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
2
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3
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1.2k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
2
votes
1
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770
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by ▴ 20
201 results • Page 1 of 5
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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.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
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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