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Showing :
edgeR
•
reset
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 weeks ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 5 months ago by
Gordon Smyth
50k • written 8.3 years ago by
Radek
▴ 90
7
votes
2
replies
890
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
6
votes
7
replies
983
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 7 months ago by
ATpoint
★ 4.2k • written 7 months ago by
jonas.freimuth
▴ 20
6
votes
2
replies
754
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
10 months ago
Josué
▴ 20
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
7
replies
621
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 12 months ago by
Sabiha
▴ 20
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 9 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 4 months ago by
Shaimaa Gamal
• 0 • written 7.2 years ago by
myprogramming2016
• 0
5
votes
4
replies
441
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago
pl23
• 0
5
votes
2
replies
613
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
5
votes
6
replies
466
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 weeks ago by
ATpoint
★ 4.2k • written 6 weeks ago by
nhaus
▴ 40
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
mohammedtoufiq91
▴ 10
5
votes
3
replies
328
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 14 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Shaimaa Gamal
• 0
5
votes
3
replies
758
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Jack S.
▴ 50
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 7 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
4
votes
6
replies
489
views
FilterByExpr low counts with small sample size
edgeR
5 weeks ago • updated 4 weeks ago
Jonathan
▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 3.6 years ago by
ATpoint
★ 4.2k
4
votes
2
replies
650
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
21 days ago • updated 17 days ago
gene_bioconductor
▴ 10
4
votes
4
replies
468
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
66k • written 4 months ago by
Geo
• 0
4
votes
3
replies
1.1k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
garcia
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 23 months ago by
Mohamed
▴ 30
4
votes
2
replies
690
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago
Luca
• 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
10 months ago
Luca
• 0
3
votes
3
replies
583
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
8 months ago
Nisha
• 0
3
votes
2
replies
690
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
CDSPARKS
▴ 10
3
votes
3
replies
742
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Jurgen
• 0
3
votes
1
reply
1.8k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR
RnaSeqSampleSizeData
RNAseq
updated 4 months ago by
Gordon Smyth
50k • written 3.1 years ago by
Lucy
▴ 60
3
votes
3
replies
372
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
3
votes
6
replies
868
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by
Dimitris
• 0 • written 10.9 years ago by
Makis Motakis
▴ 30
3
votes
3
replies
599
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 8 months ago by
James W. MacDonald
66k • written 8 months ago by
stuartthafass
• 0
3
votes
2
replies
517
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
3
votes
4
replies
550
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Jack S.
▴ 50
3
votes
5
replies
422
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Fabian
• 0
2
votes
3
replies
172
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
Guillermo
• 0
2
votes
6
replies
450
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago
tsl0026
• 0
2
votes
4
replies
666
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
2
votes
1
reply
617
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 12 months ago by
ATpoint
★ 4.2k • written 12 months ago by
calvincornell1996
• 0
2
votes
3
replies
317
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
JKim
• 0
2
votes
2
replies
294
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
10 weeks ago
Sabiha
▴ 20
2
votes
3
replies
398
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger
deseq2
updated 9 months ago by
marjim
• 0 • written 6.4 years ago by
nyoungb2
• 0
2
votes
2
replies
116
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
2 days ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
847
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 9 months ago by
Vitor
• 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 15 months ago by
Rebekah
• 0
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.1 years ago by
Marianna
▴ 20
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
10 months ago
mohammedtoufiq91
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
by
jovel_juan
▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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