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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
9 months ago mohammedtoufiq91 ▴ 10
3
votes
6
replies
843
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 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 50k • written 11 months ago by ▴ 10
3
votes
9
replies
1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
657
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 14 months ago by 50k • written 14 months ago by ▴ 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
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 17 days ago by • 0 • written 15 months ago by ▴ 10
2
votes
5
replies
3.2k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 15 months ago by 50k • written 16 months ago by ▴ 10
3
votes
6
replies
997
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
17 months ago • updated 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
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
761
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
787
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
3.5k
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
835
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 17 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 50k • written 23 months ago by ▴ 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
1.4k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 2.8 years ago by ▴ 80 • written 2.8 years ago by ▴ 10
0
votes
2
replies
1.9k
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
695
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 ▴ 260 • written 4.6 years ago by ▴ 10
1
vote
4
replies
1.5k
views
Merging two files based on the identifier column (gene symbols)?
merge files R packages gene annotations
4.7 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 ▴ 30 • written 4.7 years ago by ▴ 10
1
vote
2
replies
820
views
Support for import of custom matrix data in the ddCt R package
ddCt import analysis R qRTPCR
updated 4.7 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
0
votes
0
replies
729
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
970
views
Creation of qPCRset in R for HtqPCR
R bioconductor htqpcr qpcrset object
5.6 years ago mohammedtoufiq91 ▴ 10
29 results • Page 1 of 1
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