Showing : edger • reset
2
votes
10
replies
251
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 4 days ago by 47k • written 8 days ago by • 0
3
votes
5
replies
151
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 8 days ago by 39k • written 9 days ago by ▴ 10
0
votes
1
reply
68
views
Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 11 days ago by 39k • written 11 days ago by • 0
3
votes
2
replies
106
views
Help with the design matrix for longitudinal study
edgeR
17 days ago sharvari gujja ▴ 40
1
vote
3
replies
179
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 22 days ago by 39k • written 4 weeks ago by • 0
0
votes
2
replies
124
views
Orange point meaning in plotSmear with edgeR
edgeR plotSmear
23 days ago • updated 22 days ago Tess • 0
0
votes
3
replies
144
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
4 weeks ago • updated 29 days ago ubjw24 • 0
0
votes
1
reply
99
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
1
vote
1
reply
92
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
2
votes
5
replies
218
views
Create the design matrix
DEGseq edgeR RNASeq
5 weeks ago Mohammad • 0
0
votes
2
replies
178
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suggest to report differential estimate in edgeR
edgeR
5 weeks ago • updated 23 days ago Yongqing • 0
0
votes
4
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294
views
What function in edgeR normalize the reads between samples?
edgeR
5 weeks ago 冠宇 • 0
2
votes
4
replies
292
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
5 weeks ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
137
views
Inccorect group number in DGEList
edgeR Bioconductor Dseq2 dgelist
updated 6 weeks ago by 47k • written 6 weeks ago by • 0
0
votes
0
replies
169
views
Installing edgeR on M1 mac
edgeR
6 weeks ago Onur • 0
0
votes
2
replies
206
views
I need help with EdgeR!
edgeR
updated 6 weeks ago by ★ 2.1k • written 6 weeks ago by • 0
0
votes
2
replies
380
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 7 weeks ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
232
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 7 weeks ago by • 0 • written 10 weeks ago by ▴ 70
0
votes
0
replies
101
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
7 weeks ago Bogdan ▴ 660
3
votes
6
replies
259
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
7 weeks ago mohammedtoufiq91 ▴ 10
4
votes
6
replies
239
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
8 weeks ago Abdul ▴ 10
5
votes
6
replies
306
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
8 weeks ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
164
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
193
views
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 9 weeks ago by 47k • written 9 weeks ago by • 0
0
votes
1
reply
231
views
unable to load edgeR after installing it
edgeR
updated 9 weeks ago by ★ 2.1k • written 9 weeks ago by • 0
2
votes
4
replies
374
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
9 weeks ago mohammedtoufiq91 ▴ 10
1
vote
12
replies
605
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 9 weeks ago by 39k • written 12 weeks ago by ▴ 660
0
votes
3
replies
234
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 9 weeks ago by 47k • written 10 weeks ago by • 0
3
votes
6
replies
299
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 10 weeks ago by • 0
2
votes
5
replies
321
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR RNAseq123
updated 8 weeks ago by 47k • written 10 weeks ago by 50
1
vote
2
replies
194
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
11 weeks ago • updated 10 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
133
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 11 weeks ago by ★ 2.1k • written 11 weeks ago by • 0
3
votes
6
replies
338
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
11 weeks ago • updated 10 weeks ago Sara • 0
0
votes
4
replies
257
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
12 weeks ago • updated 11 weeks ago Amit Indap ▴ 10
3
votes
7
replies
466
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3 months ago by 47k • written 3 months ago by • 0
2
votes
1
reply
174
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3 months ago by 47k • written 3 months ago by ▴ 10
1
vote
4
replies
251
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA gene RNASeqRData edgeR geneontology
3 months ago faiza • 0
2
votes
4
replies
314
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 9 weeks ago by ★ 4.6k • written 3 months ago by ▴ 660
1
vote
7
replies
365
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 7 weeks ago by • 0 • written 3 months ago by ▴ 660
0
votes
1
reply
468
views
installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3 months ago Bogdan ▴ 660
0
votes
1
reply
306
views
bigwig to counts
DESeq2 edgeR bigwig limma
3 months ago • updated 16 days ago Bogdan ▴ 660
1
vote
4
replies
304
views
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
0
votes
9
replies
517
views
edgeR contrasts
edgeR
4 months ago ignadb • 0
3
votes
6
replies
469
views
variance decomposition formula
edgeR
5 months ago Xinwei • 0
-6
votes
4
replies
311
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
5 months ago Mike • -60
1
vote
1
reply
178
views
How to interpret FC and pesudocounts in EDGER using glmLRT?
edgeR
updated 5 months ago by 47k • written 5 months ago by • 0
0
votes
0
replies
129
views
Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
5 months ago Jonathan • 0
1
vote
4
replies
618
views
TPM normalization starting with read counts
edgeR DESeq2
updated 5 months ago by 47k • written 5 months ago by • 0
3
votes
4
replies
508
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 6 months ago by 47k • written 6 months ago by ▴ 10
1
vote
1
reply
234
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 6 months ago by 47k • written 6 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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