Showing : EdgeR • reset
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cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
5
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6
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1.9k
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 6.1 years ago by ▴ 900 • written 6.1 years ago by ▴ 10
0
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1
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2.0k
views
Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
deseq2 normalization RUVg edger
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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3
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1.6k
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Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by ▴ 80
0
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2
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1.7k
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How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
6.1 years ago fgol ▴ 10
0
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2
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672
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Searching for responsive genes along with a continuous variable, in environmental experimental design
edger
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
2
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1
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1.3k
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edgeR default normalization method
edger
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
1
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6
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2.9k
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Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.1 years ago sabrina.mcnew • 0
1
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1
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1.5k
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Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
6.2 years ago konstantinos.bogias ▴ 10
0
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4
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917
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The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
0
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1
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436
views
Sai Nikhith Cholleti
edger deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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6
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2.3k
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by ▴ 670
1
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4
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1.0k
views
Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
2
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2
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1.5k
views
How to create two columns for model matrix used in limma?
limma edger
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 60
8
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5
replies
5.4k
views
the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
normalization DESeq2 edgeR
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 10
7
votes
4
replies
3.1k
views
RNA-seq normalization without filtering
deseq2 edger normalization RNAseq
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 50
1
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5
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4.6k
views
how to get normalized count data from edgeR using TMM methods
edger normalization
6.2 years ago 15958021290 ▴ 10
0
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4
replies
1.4k
views
design matrix for 4 groups in edgeR
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
0
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0
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913
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News: Course in Berlin- Genomics with R and Bioconductor - September 16-20
deseq2 edger limma News
6.2 years ago info ▴ 10
0
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4
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4.7k
views
edgeR DGEList and design matrix
edger DGE
updated 6.2 years ago by ▴ 900 • written 6.2 years ago by • 0
0
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3
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1.1k
views
Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
limma edger normalization
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 280
0
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4
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3.0k
views
EdgeR mistake- dispersion
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
6
votes
10
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6.5k
views
goana and "No annotated genes found in universe" even with Entrez gene ids
goana edger
updated 3.7 years ago by 53k • written 6.2 years ago by ▴ 10
4
votes
4
replies
3.6k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
4
votes
4
replies
1.3k
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
1
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4
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1.2k
views
Feedback on edgeR model setup: identifying sex-by-tissue effects
edger
updated 6.2 years ago by ★ 29k • written 6.2 years ago by • 0
2
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6
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2.6k
views
RNA-Seq normalization for co-expression analysis
edger WGCNA limma
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 50
6
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6
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1.5k
views
EdgeR - Model matrix for complex model similar to user guide 3.5 example - but more complex
edger limma
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 10
5
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18
replies
2.7k
views
Difference of difference, paired design
edger deseq2 limma
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by • 0
1
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4
replies
1.5k
views
Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma deseq2 edgeR
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 50
0
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0
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1.0k
views
adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
4
votes
3
replies
1.4k
views
Complex multifactorial design with random effects in Limma/voom
limma edger
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 20
0
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4
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3.0k
views
Why am I getting many differentially expressed genes that have no symbol or do not map to a chromosome (RNA-seq)
edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
3
votes
3
replies
2.4k
views
Differential Expression Analysis in edgeR using Anova
edger anova gene expression Dispersion
updated 6.3 years ago by • 0 • written 6.8 years ago by • 0
0
votes
3
replies
845
views
FNR in RNASeq
deseq2 edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
0
votes
2
replies
2.4k
views
Normalized count in edger
edger
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by • 0
2
votes
4
replies
1.9k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
1
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6
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3.1k
views
adjusting for confounding effects in edgeR
edger confounding
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
5
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3
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1.8k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
8
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7
replies
2.7k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 6.3 years ago by • 0 • written 7.1 years ago by ▴ 20
1
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5
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2.0k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 6.3 years ago by • 0 • written 6.3 years ago by • 0
5
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3
replies
1.6k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
6
votes
8
replies
2.5k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
6.3 years ago Jurat Shahidin ▴ 80
3
votes
7
replies
4.5k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq DGE edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
1
vote
12
replies
2.1k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 90
0
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0
replies
1.2k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.3 years ago garbuzov • 0
0
votes
2
replies
3.2k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 6.4 years ago by ▴ 980 • written 6.5 years ago by • 0
0
votes
3
replies
1.5k
views
phyloseq to edgeR
edger
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 10
0
votes
1
reply
571
views
Test genes expressed ( not just expressed higher ) in one or two group
limma edger
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 30
5
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7
replies
3.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
6.4 years ago altintas.ali • 0
2,031 results • Page 12 of 41
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Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by umairmugal82 • 0
When accuracy matters in academic assessment, nothing should be left to chance. [Accurate grading made simple on EasyGrader.net][1] ensures…
Votes
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
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