Showing : EDGER • reset
1
vote
9
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4.7k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 2.9 years ago by ▴ 670 • written 5.0 years ago by ▴ 10
0
votes
1
reply
649
views
Using DESEQ/EdgeR for estimating differential expression relative to a control.
edgeR DifferentialExpression
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
1
reply
912
views
edgeR rrbs estimateDisp runs forever and doesn't seem to finish
edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
1
vote
1
reply
2.1k
views
DiffBind for ATAC-Seq count extraction
esATAC edgeR DiffBind
updated 5.0 years ago by ★ 5.2k • written 5.0 years ago by • 0
2
votes
2
replies
1.3k
views
log transform or not the dependent variable/ covariates
limma edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 40
4
votes
10
replies
2.1k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.0 years ago Hajar • 0
2
votes
2
replies
1.3k
views
Paired analysis adjusted for RIN value
limma edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 40
4
votes
3
replies
2.5k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 24 months ago by 53k • written 5.0 years ago by ★ 5.0k
9
votes
10
replies
9.6k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.6 years ago by ▴ 20 • written 5.0 years ago by ▴ 10
1
vote
0
replies
645
views
Differential gene expression associated with metabolite levels following diet
edger
5.0 years ago anna.cot.anna.cot ▴ 40
1
vote
3
replies
921
views
filter factor DGEList
edger
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
2
votes
3
replies
1.3k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
votes
7
replies
3.6k
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 5.1 years ago by ▴ 900 • written 5.1 years ago by • 0
0
votes
2
replies
1.8k
views
edgeR for single-cell data with inferential replicates
edgeR alevin
5.1 years ago ATpoint ★ 5.0k
2
votes
5
replies
1.9k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq limma edgeR
updated 14 months ago by • 0 • written 5.1 years ago by ▴ 10
0
votes
8
replies
1.8k
views
Designating contrasts in diffSpliceDGE to test for nested effects
diffSpliceDGE Contrast matrix edger
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
3
votes
3
replies
1.5k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 10
1
vote
1
reply
822
views
In edgeR, how am I supposed to be gauging the results of the BCV Plots, the values of common dispersion, tagwise disperson, ect.
edger
5.1 years ago science555111 • 0
10
votes
10
replies
2.4k
views
RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
limma edger
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 10
3
votes
1
reply
1.2k
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
5
votes
2
replies
964
views
Differential gene expression associated with change in blood parameter following diet
edger
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 40
6
votes
4
replies
1.4k
views
edgeR and batch effects
edger
updated 5.1 years ago by ★ 13k • written 5.1 years ago by ▴ 10
6
votes
5
replies
2.4k
views
Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
updated 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
3
votes
6
replies
1.5k
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1
vote
1
reply
791
views
technical replicates in WGCNA
edger
updated 5.1 years ago by ★ 3.0k • written 5.1 years ago by • 0
9
votes
4
replies
1.7k
views
TMM normalization on sparse datasets
edger limma
5.1 years ago jc235601 ▴ 20
2
votes
4
replies
9.9k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
1
vote
2
replies
1.3k
views
eisaR settings for three biological replicates
eisaR edgeR
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
2
votes
2
replies
2.0k
views
RNA-Seq Time series analysis in EdgeR
edger Time series analysis
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 10
1
vote
3
replies
4.6k
views
TMM normalized matrix from count matrix using edgeR
edger
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
votes
1
reply
676
views
do cox and km plot
limma edger
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 20
0
votes
2
replies
1.0k
views
How to normalise data in ballgown?
r normalization edger
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
6
replies
1.2k
views
The coefficients not estimable
edger
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 420
2
votes
4
replies
2.7k
views
Minimum required samples for RNA-seq differential Analysis?
deseq2 limma edger
5.2 years ago linouhao ▴ 20
0
votes
2
replies
4.2k
views
CPM function in EDGER
edger cpm rnaseq
5.2 years ago francesca3 • 0
0
votes
2
replies
818
views
Custom dispersion estimate DESeq2
deseq2 edger
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 110
1
vote
7
replies
2.2k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 30
6
votes
13
replies
7.8k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 3.3 years ago by 53k • written 5.2 years ago by ▴ 60
6
votes
4
replies
4.0k
views
Having TMM for GSEA
edger deseq2
updated 4.6 years ago by ★ 4.0k • written 5.2 years ago by ▴ 30
5
votes
8
replies
1.9k
views
Not seeing gene ID in glmQLFit headers
glmQLFit edgeR header
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
votes
1
reply
956
views
Regression Analysis between RNA-seq data and expression measured from ELISA
limma edger
5.2 years ago Bioinformatician_R ▴ 20
2
votes
8
replies
2.8k
views
Differential gene expression using R
deseq2 edger normalization limma
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
8
votes
11
replies
1.9k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger rnaseq
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 10
2
votes
2
replies
916
views
Can edgeR be used to calculate the foldchange difference of GOs / KEGG terms/ Or even microbe abundance?
edger
5.2 years ago megha.hs28 ▴ 10
2
votes
2
replies
1.9k
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
votes
2
replies
1.4k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 5.2 years ago by 53k • written 5.3 years ago by • 0
4
votes
3
replies
578
views
Average Effect in edgeR
edgeR
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
2
votes
2
replies
1.1k
views
In EdgeR TMM and/or voom is it better to normalize all samples, even if some will not be used for comparisons?
edger limma
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 60
2
votes
3
replies
2.5k
views
"Error in xy.coords(x, y, setLab = FALSE) : 'x' and 'y' lengths differ" using glmQLFit
glmQLFit edger
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
4
votes
7
replies
1.8k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
2,031 results • Page 9 of 41
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Comment: "Watched Tags" are being erased rather than updated by dipakosikotes • 0
Possibly a combination: some change in the forum software that affects some accounts/configurations but not all [unblocked games][1] […
Answer: EuroBioC2023 abstract submission is open! by Hao • 0
It's obvious that the blogger hought on details. It is not only easy to read but also makes the content more rich and interesting.[1v1 …
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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