Showing : edgeR • reset
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
1 hour ago Ashley • 0
5
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3
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287
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Log-cpm values from limma
limma edgeR RNASeq
updated 3 days ago by 50k • written 25 days ago by • 0
4
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2
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599
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
11 days ago • updated 7 days ago gene_bioconductor ▴ 10
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1
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157
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 11 days ago by 50k • written 11 days ago by • 0
1
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1
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186
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Citation for edgeR user guide
edgeR
updated 20 days ago by 50k • written 20 days ago by ▴ 30
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6
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449
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FilterByExpr low counts with small sample size
edgeR
26 days ago • updated 21 days ago Jonathan ▴ 10
3
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3
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358
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permutation test in edgeR
rna-seq edgeR
updated 22 days ago by 50k • written 5 weeks ago by • 0
6
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10
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1.7k
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Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 24 days ago by • 0 • written 15 months ago by ▴ 10
0
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3
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201
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 24 days ago by 50k • written 25 days ago by • 0
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2
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142
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
24 days ago prity6459 • 0
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 25 days ago by • 0 • written 8.8 years ago by ▴ 30
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3
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359
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 28 days ago by 50k • written 4 weeks ago by • 0
5
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6
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446
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by ▴ 30
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3
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271
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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2
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184
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
5 weeks ago Marianna ▴ 20
0
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4
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442
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago • updated 5 weeks ago Lucy ▴ 60
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5
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1.8k
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EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 5 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
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5
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401
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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1.1k
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library size and fold changes
edgeR edgeR
updated 6 weeks ago by 50k • written 12.4 years ago by ▴ 670
0
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6
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366
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
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3
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727
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
0
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1
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246
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
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3
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302
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
2
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2
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265
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between lane normalization upper quantile
EDASeq edgeR
8 weeks ago elesofi • 0
0
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2
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295
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
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2
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276
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
1
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3
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431
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
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4
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469
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 50
0
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11
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761
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
0
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1
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230
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
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1
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271
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ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
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5
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1.4k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
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6
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517
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Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago • updated 10 weeks ago mico • 0
5
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4
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414
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Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
0
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8
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669
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 11 weeks ago Marianna ▴ 20
2
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6
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431
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago tsl0026 • 0
3
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2
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474
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
1
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2
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336
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
0
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4
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359
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
2
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3
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381
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
3
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4
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8.6k
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Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
1
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8
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558
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
4
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4
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445
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
0
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5
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634
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
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7
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589
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readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
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0
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257
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
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4
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616
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
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3
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356
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
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3
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694
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
4
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9
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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago • updated 3 months ago Luca • 0
50 results • Page 1 of 1
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Answer: Store output of matchPWM() by mat149 ▴ 70
hitlist<-lapply(irs, FUN = matchPWM, min.score="90%", with.score=TRUE, pwm = pwm) ot <- endoapply(hitlist, function(x) as(x, "IRanges")) …
Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by alex.pico ▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Votes
Comment: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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