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edger
•
reset
0
votes
2
replies
919
views
suggest to report differential estimate in edgeR
edgeR
3.1 years ago • updated 3.0 years ago
Yongqing
• 0
0
votes
4
replies
1.3k
views
What function in edgeR normalize the reads between samples?
edgeR
3.1 years ago
冠宇
• 0
4
votes
5
replies
6.7k
views
How to identify top most variable genes from log2 normalized data?
supervised
edgeR
variance
RNASeq
heatmaps
updated 3.0 years ago by
Gordon Smyth
53k • written 3.1 years ago by
mohammedtoufiq91
▴ 10
2
votes
2
replies
1.1k
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
Fiona
• 0
0
votes
0
replies
862
views
Installing edgeR on M1 mac
edgeR
3.1 years ago
Onur
• 0
0
votes
2
replies
917
views
I need help with EdgeR!
edgeR
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
marta.lagana
• 0
0
votes
2
replies
1.5k
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR
DESeq2
updated 3.1 years ago by
chaco001
• 0 • written 3.6 years ago by
nc2849
• 0
0
votes
2
replies
1.4k
views
TnSeq as ZINB? Alternatives in R?
DESeq2
R
edgeR
Python
TnSeq
updated 3.1 years ago by
chaco001
• 0 • written 3.2 years ago by
David R
▴ 90
0
votes
0
replies
830
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma
edgeR
csaw
3.1 years ago
Bogdan
▴ 670
3
votes
6
replies
1.9k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
3.1 years ago
mohammedtoufiq91
▴ 10
4
votes
6
replies
1.9k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
3.1 years ago
Abdul
▴ 20
5
votes
6
replies
3.6k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
3.1 years ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
3.1 years ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
2.4k
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 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
Isa
• 0
0
votes
1
reply
1.6k
views
unable to load edgeR after installing it
edgeR
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Vittorio
• 0
2
votes
4
replies
6.1k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
3.1 years ago
mohammedtoufiq91
▴ 10
1
vote
12
replies
3.9k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2
edgeR
limma
updated 3.1 years ago by
Michael Love
43k • written 3.2 years ago by
Bogdan
▴ 670
1
vote
3
replies
1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 3.1 years ago by
Gordon Smyth
53k • written 3.2 years ago by
wiscoyogi
• 0
3
votes
6
replies
2.2k
views
One-tailed test edgeR possible?
one-tailed
edgeR
DifferentialExpression
test
written 3.2 years ago by
Sarah
• 0
2
votes
5
replies
1.8k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 3.1 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Istvan Albert
▴ 50
1
vote
2
replies
1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
3.2 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
Jenni
• 0
3
votes
6
replies
3.6k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2
edgeR
RNA
limma
Normalization
3.2 years ago
Sara
• 0
0
votes
4
replies
1.7k
views
paired tests with tidybulk and edgeR
edgeR
R
tidyverse
tidybulk
3.2 years ago
Amit Indap
▴ 10
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r
rnaseq
DifferentialExpression
limma
edger
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
jirkamanuel.petersen
• 0
2
votes
1
reply
1.1k
views
Different sequencing depth between replicates and samples
DESeq2
edgeR
DiffBind
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
cesar.arenasmena
▴ 10
1
vote
4
replies
1.6k
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA
gene
RNASeqRData
edgeR
geneontology
3.2 years ago
faiza
• 0
2
votes
4
replies
1.7k
views
DiffBind and peak counts as input
DESeq2
edgeR
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Bogdan
▴ 670
1
vote
7
replies
1.8k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2
edgeR
updated 3.1 years ago by
chaco001
• 0 • written 3.3 years ago by
Bogdan
▴ 670
1
vote
1
reply
3.6k
views
installation of BioC packages on Mac M1 Monterrey OS
limma
Bioconductor
edgeR
3.3 years ago
Bogdan
▴ 670
0
votes
1
reply
2.6k
views
bigwig to counts
DESeq2
edgeR
bigwig
limma
3.3 years ago • updated 3.0 years ago
Bogdan
▴ 670
1
vote
4
replies
2.0k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 3.3 years ago by
Simon Pearce
• 0 • written 3.3 years ago by
a.riediger
▴ 20
0
votes
11
replies
5.7k
views
edgeR contrasts
edgeR
updated 2.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
ignadb
• 0
3
votes
6
replies
2.2k
views
variance decomposition formula
edgeR
3.4 years ago
Xinwei
• 0
-6
votes
4
replies
1.3k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast
edgeR
DEGs
3.4 years ago
Mike
• -60
1
vote
1
reply
917
views
How to interpret FC and pesudocounts in EDGER using glmLRT?
edgeR
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
rimelof
• 0
0
votes
0
replies
919
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
3.4 years ago
Jonathan
• 0
1
vote
4
replies
10.0k
views
TPM normalization starting with read counts
edgeR
DESeq2
updated 3.4 years ago by
Gordon Smyth
53k • written 3.4 years ago by
JAcky
• 0
3
votes
4
replies
1.5k
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
Claire.Prince
▴ 10
1
vote
1
reply
1.4k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
e.g.w.miller
▴ 10
3
votes
4
replies
3.8k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
3.5 years ago
Yang Shi
▴ 10
5
votes
8
replies
28k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 17 months ago by
Ahdee
▴ 60 • written 3.6 years ago by
Mohamed
▴ 30
1
vote
3
replies
3.2k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
BG
• 0
0
votes
4
replies
3.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
3.6 years ago
Mohamed
▴ 30
1
vote
8
replies
2.4k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression
celltype
treatment
edgeR
limma
3.6 years ago
giBio
• 0
0
votes
1
reply
1.8k
views
dispersion in edgeR
Sequencing
edgeR
Sequencing
edgeR
updated 3.6 years ago by
Gordon Smyth
53k • written 15.6 years ago by
Naomi Altman
★ 6.0k
0
votes
2
replies
1.6k
views
Locating nearest genes in RRBS analysis
hiAnnotator
bsseq
DifferentialMethylation
edgeR
RRBSdata
3.7 years ago • updated 3.6 years ago
Mageiros
• 0
3
votes
2
replies
1.6k
views
time-series analysis using EdgeR
timecourse
edgeR
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
Mug_qd
• 0
2
votes
3
replies
3.1k
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R
edgeR
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
Mohamed
▴ 30
2
votes
2
replies
1.4k
views
Help with constructing design matrix for edgeR/limma
limma
design.matrix
model.matrix
edgeR
3.7 years ago • updated 3.6 years ago
adrianna_07
• 0
2,035 results • Page
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
ATpoint
★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening in a clean install
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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