Showing : EDGER • reset
1
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6
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1.1k
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EdgeR analysis of bottlenecked genetic screen data
edgeR
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 10
1
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2
replies
1.0k
views
How to extract genes with greatest BCV?
edger
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
8
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12
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13k
views
EdgeR: Explaning dispersion types to newbies
edger dispersion estimatedispersions visualization teaching
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 20
3
votes
4
replies
2.7k
views
Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
edgeR r bioconductor diffferential expression fdr
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 120
3
votes
3
replies
983
views
edgeR: setting up proper contrasts for interactions
edger limma
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
7
votes
15
replies
7.6k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 60
1
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2
replies
2.2k
views
How to change sample names in featureCounts or edgeR
featurecounts edgeR
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 20
19
votes
6
replies
36k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR cpm
updated 7.4 years ago by ▴ 20 • written 7.6 years ago by ▴ 40
2
votes
1
reply
1.2k
views
EdgeR - How to set up the design matrix for a multifactorial experimental design with interactions?
edger edger main and interaction effects glmfit
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 10
2
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3
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1.8k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 2.6 years ago by 53k • written 7.4 years ago by ▴ 20
2
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7
replies
5.1k
views
edgeR for continuous independent variables
edger
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 20
1
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1
reply
1.6k
views
post hoc analysis on nested model
nested design post hoc edgeR
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
4
votes
5
replies
7.1k
views
Up/Down Regulated GeneList from edgeR and R
edger R Up reg genelist
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
7
votes
6
replies
7.3k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 60
6
votes
5
replies
1.6k
views
How to obtain a normalised expression matrix from read counts and scaling factors
edger
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 30
2
votes
2
replies
1.6k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
5
votes
4
replies
3.4k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 4.4 years ago by 53k • written 7.5 years ago by ▴ 120
2
votes
9
replies
1.8k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ▴ 20
3
votes
4
replies
2.1k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by ▴ 20
0
votes
0
replies
931
views
processAmplicons to match sequences 1 or 2 bases shorter than guides?
processamplicons edgeR
updated 7.5 years ago by 4.2k • written 7.5 years ago by • 0
4
votes
4
replies
2.2k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
0
votes
1
reply
1.9k
views
EdgeR: run processAmplicons without barcodes
EdgeR CRISPR Barcode processamplicons
updated 7.5 years ago by • 0 • written 8.7 years ago by • 0
3
votes
7
replies
2.3k
views
single continuous factor
edger design matrix continuous
updated 3.7 years ago by • 0 • written 7.5 years ago by • 0
6
votes
14
replies
4.1k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 840
2
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2
replies
1.9k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
7.5 years ago shankasal • 0
5
votes
12
replies
9.4k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 120
0
votes
5
replies
1.4k
views
edgeR and DESeq2
edger deseq2
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 20
4
votes
2
replies
1.9k
views
how to calculate the logFC value
edger
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 20
2
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2
replies
1.1k
views
no replicates data
edger
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 20
3
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4
replies
1.8k
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
5
votes
5
replies
1.3k
views
Nested design in edgeR
edger
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
3
votes
6
replies
5.8k
views
Principle component analysis plot with gene expression data
r pca rnaseq edger ggbiplot
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 120
3
votes
3
replies
10k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 3.5 years ago by 53k • written 7.5 years ago by • 0
6
votes
9
replies
7.1k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
5
votes
4
replies
1.7k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
0
votes
1
reply
737
views
Do we include unclassified reads (and other ambiguous reads) in normalization
edger normalization
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
5
votes
6
replies
1.4k
views
AveLogCPM of a library subset
edger rnaseq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
1
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9
replies
2.1k
views
Comparison between limma and edgeR of reads ratio
edgeR limma offset
updated 7.5 years ago by 53k • written 7.6 years ago by • 0
3
votes
5
replies
2.2k
views
EdgeR: Prior degrees of freedom effect on tag wise dispersion
R edgeR rnaseq rna-seq
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 20
1
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5
replies
1.5k
views
how to create csv file with name of gene from unique ID of lcpm ?
edgeR lcpm bioconductor
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
4
votes
8
replies
2.2k
views
edgeR error when trying to filter peaks with low read counts
edger R filtering
7.6 years ago camerond • 0
1
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4
replies
3.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR summarizedexperiment dgelist
7.6 years ago aljoscha.leusmann • 0
4
votes
4
replies
1.8k
views
edgeR: Choice of reference group in nested model
edgeR model.matrix nested design reference group
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 40
8
votes
4
replies
1.3k
views
read counts for gene families
edger
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 10
4
votes
4
replies
2.2k
views
Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes
updated 7.6 years ago by • 0 • written 7.6 years ago by ▴ 60
5
votes
1
reply
1.1k
views
edgeR normalisation factors different between experimental groups
edger
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 180
1
vote
5
replies
1.8k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.6 years ago David R ▴ 90
3
votes
2
replies
2.0k
views
Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
edgeR rnaseq repeated measures
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by • 0
0
votes
2
replies
1.5k
views
Differential expression testing for groups with unequal variances/dispersions?
edgeR edgeR
updated 7.6 years ago by ▴ 10 • written 12.5 years ago by ★ 7.9k
2,031 results • Page 16 of 41
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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