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Showing :
questions
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
3
votes
6
replies
828
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 10 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
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 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
9
replies
1.7k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
13 months ago • updated 12 months ago
mohammedtoufiq91
▴ 10
2
votes
2
replies
643
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
mohammedtoufiq91
▴ 10
6
votes
11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR
DifferentialExpression
limma
design
RNASeq
14 months ago
mohammedtoufiq91
▴ 10
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
2
votes
5
replies
3.1k
views
How to identify top most variable genes from log2 normalized data?
supervised
edgeR
variance
RNASeq
heatmaps
updated 14 months ago by
Gordon Smyth
50k • written 16 months ago by
mohammedtoufiq91
▴ 10
3
votes
6
replies
978
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
5
votes
6
replies
1.7k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM
filterByExpr
edgeR
histogram
rowsums
16 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
745
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
781
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
17 months ago • updated 16 months ago
mohammedtoufiq91
▴ 10
2
votes
4
replies
3.4k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
17 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
827
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
17 months ago
mohammedtoufiq91
▴ 10
5
votes
8
replies
1.9k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
19 months ago • updated 16 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
1.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
mohammedtoufiq91
▴ 10
4
votes
6
replies
1.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
23 months ago
mohammedtoufiq91
▴ 10
3
votes
4
replies
1.3k
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
2.0 years ago
mohammedtoufiq91
▴ 10
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 4 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.1k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.8 years ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.8k
views
How to adjust and align timepoints on x-axis in the ggplot2
ggplot2
line plot
x-axis
data frame
R
4.4 years ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
686
views
Unable to obtain the line chart with error envelop in ggplot2 and geom_ribbon()
ggplot2
line chart
R
geom_ribbon()
4.6 years ago
mohammedtoufiq91
▴ 10
3
votes
7
replies
3.2k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix
heatmap
ComplexHeatmap
missing values
R
updated 4.6 years ago by
Zuguang Gu
▴ 260 • written 4.6 years ago by
mohammedtoufiq91
▴ 10
1
vote
4
replies
1.5k
views
Merging two files based on the identifier column (gene symbols)?
merge
files
R
packages
gene annotations
4.6 years ago
mohammedtoufiq91
▴ 10
2
votes
4
replies
1.1k
views
Are there any functions to subtract all features(rows) to a particular value(row) in the same data file?
R
python
normalization
matrix
updated 4.7 years ago by
shahryary
▴ 30 • written 4.7 years ago by
mohammedtoufiq91
▴ 10
1
vote
2
replies
811
views
Support for import of custom matrix data in the ddCt R package
ddCt
import
analysis
R
qRTPCR
updated 4.7 years ago by
Zhang, Jitao David
▴ 120 • written 4.7 years ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
721
views
Sample grouping (phenoData) and visualization in R package- HtqPCR
HtqPCR
grouping
visualization
R
phenoData
4.7 years ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
963
views
Creation of qPCRset in R for HtqPCR
R
bioconductor
htqpcr
qpcrset object
5.6 years ago
mohammedtoufiq91
▴ 10
29 results • Page
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