Showing : EdgeR • reset
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 6 hours ago by 47k • written 14 hours ago by • 0
3
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5
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102
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Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 12 hours ago by 39k • written 1 day ago by ▴ 10
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1
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54
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Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 3 days ago by 39k • written 3 days ago by • 0
3
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2
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92
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Help with the design matrix for longitudinal study
edgeR
9 days ago sharvari gujja ▴ 40
1
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3
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164
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 14 days ago by 39k • written 22 days ago by • 0
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2
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111
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Orange point meaning in plotSmear with edgeR
edgeR plotSmear
15 days ago • updated 14 days ago Tess • 0
0
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3
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135
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Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
22 days ago • updated 21 days ago ubjw24 • 0
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1
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88
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Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 27 days ago by 47k • written 27 days ago by • 0
1
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1
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83
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Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 27 days ago by 47k • written 27 days ago by • 0
2
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5
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197
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Create the design matrix
DEGseq edgeR RNASeq
29 days ago • updated 28 days ago Mohammad • 0
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2
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168
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suggest to report differential estimate in edgeR
edgeR
4 weeks ago • updated 15 days ago Yongqing • 0
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4
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285
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What function in edgeR normalize the reads between samples?
edgeR
4 weeks ago 冠宇 • 0
2
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4
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279
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How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
4 weeks ago mohammedtoufiq91 ▴ 10
2
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2
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132
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Inccorect group number in DGEList
edgeR Bioconductor Dseq2 dgelist
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
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156
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Installing edgeR on M1 mac
edgeR
5 weeks ago Onur • 0
0
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2
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201
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I need help with EdgeR!
edgeR
updated 5 weeks ago by ★ 2.0k • written 5 weeks ago by • 0
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2
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361
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Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 6 weeks ago by • 0 • written 7 months ago by • 0
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2
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223
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TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 6 weeks ago by • 0 • written 9 weeks ago by ▴ 70
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97
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
6 weeks ago Bogdan ▴ 660
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6
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251
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
6 weeks ago mohammedtoufiq91 ▴ 10
4
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6
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235
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Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
6 weeks ago Abdul ▴ 10
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6
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294
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How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
7 weeks ago mohammedtoufiq91 ▴ 10
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2
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152
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
7 weeks ago mohammedtoufiq91 ▴ 10
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2
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162
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Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR edge
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
0
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1
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204
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unable to load edgeR after installing it
edgeR
updated 8 weeks ago by ★ 2.0k • written 8 weeks ago by • 0
2
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4
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327
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
8 weeks ago mohammedtoufiq91 ▴ 10
1
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12
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560
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normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 8 weeks ago by 39k • written 10 weeks ago by ▴ 660
0
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3
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226
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diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
3
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6
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292
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 9 weeks ago by • 0
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5
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313
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Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR RNAseq123
updated 7 weeks ago by 47k • written 9 weeks ago by 50
1
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2
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187
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
9 weeks ago mohammedtoufiq91 ▴ 10
0
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1
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118
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Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 9 weeks ago by ★ 2.0k • written 9 weeks ago by • 0
3
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6
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328
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
10 weeks ago • updated 9 weeks ago Sara • 0
0
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4
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241
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paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
11 weeks ago • updated 10 weeks ago Amit Indap ▴ 10
3
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7
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449
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 11 weeks ago by 47k • written 12 weeks ago by • 0
2
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1
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160
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Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3 months ago by 47k • written 3 months ago by ▴ 10
1
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4
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243
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RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA gene RNASeqRData edgeR geneontology
3 months ago faiza • 0
2
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4
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299
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DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 8 weeks ago by ★ 4.6k • written 3 months ago by ▴ 660
1
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7
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359
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statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 6 weeks ago by • 0 • written 3 months ago by ▴ 660
0
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1
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441
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installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3 months ago Bogdan ▴ 660
0
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1
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296
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bigwig to counts
DESeq2 edgeR bigwig limma
3 months ago • updated 8 days ago Bogdan ▴ 660
1
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4
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299
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QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 4 months ago by • 0 • written 4 months ago by • 0
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9
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500
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edgeR contrasts
edgeR
4 months ago ignadb • 0
3
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6
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452
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variance decomposition formula
edgeR
4 months ago Xinwei • 0
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4
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300
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is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
4 months ago Mike • -60
1
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1
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176
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How to interpret FC and pesudocounts in EDGER using glmLRT?
edgeR
updated 5 months ago by 47k • written 5 months ago by • 0
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119
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
5 months ago Jonathan • 0
1
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4
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565
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TPM normalization starting with read counts
edgeR DESeq2
updated 5 months ago by 47k • written 5 months ago by • 0
3
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4
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502
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edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 5 months ago by 47k • written 6 months ago by ▴ 10
1
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1
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229
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Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 5 months ago by 47k • written 5 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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