Showing : EDGER • reset
5
votes
10
replies
3.3k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR differential expression analysis covariates
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 60
6
votes
2
replies
1.5k
views
tximport + edgeR not recommended?
tximport edgeR
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
6
replies
1.7k
views
Question: Method to get normalize allele specific read counts
edger normalization
updated 5.3 years ago by ★ 29k • written 5.4 years ago by • 0
1
vote
2
replies
1.2k
views
EdgeR blocking factor - missing paired sample
EdgeR edgeR RNA-seq differential expression analysis blocking factors
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 60
0
votes
2
replies
1.9k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
votes
6
replies
2.6k
views
Workaround to using normalized counts as input for edgeR
edger
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 40
1
vote
1
reply
600
views
Unable to run tximport using sample.info ?
tximport deseq2 edgeR
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
3
votes
2
replies
1.1k
views
Differential methylation analysis and paired samples
edger bisulfite sequencing
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
3
votes
4
replies
1.1k
views
DGE analysis (statistics)
edger limma
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
7
votes
10
replies
2.9k
views
is there a function in edger the same as vst or rlog in deseq2
edger normalization deseq2
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 20
0
votes
1
reply
561
views
RNA Targeted Ampliseq Data analysis - What approach to prefer?
ampliseq rna targeted edger deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 60
2
votes
7
replies
2.0k
views
How to create a matrix from a set of files containing counts for a set of attributes?
edgeR
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
2
votes
2
replies
1.4k
views
ANOVA-like test with edgeR
edger
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 60
0
votes
2
replies
1.1k
views
Differential analysis of protein spectral counts using msnSet object
annotation edger
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
4
votes
2
replies
1.2k
views
edgeR Time course analysis, choice on degree of freedom
edger
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 10
6
votes
6
replies
1.9k
views
Suggestion for next revision of edgeR User Guide re Design matrix setup
edger error
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
0
votes
3
replies
2.1k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
4
votes
6
replies
5.6k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 10
6
votes
7
replies
3.8k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 10 months ago by 53k • written 5.5 years ago by ▴ 20
0
votes
2
replies
589
views
How to find differential gene and expression analysis using DESeq or edgeR
edger deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
6
replies
2.0k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
2
votes
4
replies
1.4k
views
MEDIPS results differ with sample ordering
MEDIPS edgeR
updated 5.5 years ago by ▴ 570 • written 5.8 years ago by ▴ 60
3
votes
2
replies
3.5k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
1
vote
2
replies
1.2k
views
treating RNA-seq gene expression data in cpm for edgeR
edger
updated 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
0
votes
1
reply
594
views
Where to find the supplementary files for the case studies in edgeR User Guide
edger
updated 5.5 years ago by ★ 4.0k • written 5.6 years ago by • 0
5
votes
1
reply
2.4k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 20
0
votes
3
replies
896
views
Detection of genes associated with polymorphism
edger
5.5 years ago anna.cot.anna.cot ▴ 40
0
votes
2
replies
1.3k
views
DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2 edgeR repenrich2 normalization
5.5 years ago mkmwong • 0
3
votes
5
replies
14k
views
DESeq2 vs edgeR results analysis
deseq2 edgeR
updated 3.8 years ago by 53k • written 5.5 years ago by ▴ 40
3
votes
5
replies
2.2k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 60
6
votes
6
replies
3.1k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 60
2
votes
2
replies
3.2k
views
how to do normalization using edgeR
edger
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 40
2
votes
2
replies
1.1k
views
edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 20
0
votes
2
replies
581
views
EdgeR-Timeseries w nested design
deseq2 edger
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
1
vote
1
reply
1.3k
views
Design edger with one or more continues variables
edger
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 40
1
vote
1
reply
792
views
Differential Expression by Chromosome using edgeR
edgeR chromosome RNAseq
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by • 0
0
votes
0
replies
398
views
Removing unused samples when estimating dispersion with EdgeR?
edger
5.6 years ago elise.skottene • 0
1
vote
7
replies
1.1k
views
EdgeR design matrix question
edger
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
votes
2
replies
1.0k
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
4
votes
7
replies
1.9k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 60
1
vote
1
reply
867
views
edgeR DGEList model matrix and experiment design
edgeR
updated 5.6 years ago by ▴ 900 • written 5.6 years ago by • 0
0
votes
3
replies
2.6k
views
edgeR: "no non-missing arguments to min; returning Inf" after filterByExpression
filterByExpression edgeR RNAseq analysis edger
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
1
vote
2
replies
1.7k
views
RNAseq analysis with edgeR-interaction terms and comparison within and between groups
edger
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
1
vote
5
replies
2.0k
views
Gene Ontology analysis
ontology edger limma ncbi organism package
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 20
8
votes
5
replies
4.2k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 5.6 years ago by 53k • written 5.6 years ago by ▴ 10
5
votes
7
replies
2.8k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 2.6 years ago by ▴ 50 • written 5.7 years ago by ▴ 20
0
votes
1
reply
3.2k
views
Where in the procedure do I remove low-expressed genes?
deseq2 edger
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
2
votes
8
replies
2.3k
views
Bias towards significantly negative logFCs in ATAC-Seq differential chromatin openness tests
limma edger atac atac-seq
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 70
1
vote
2
replies
867
views
EdgeR function nearestTSS() fails saying NAs are not allowed in subscripted assignments
edgeR nearestTSS
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
votes
0
replies
907
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
5.7 years ago info ▴ 10
2,031 results • Page 10 of 41
Recent ...
Replies
Comment: After running samtools, the featureCounts command crashed. by eja.gssssse.r.m • 0
The buffer overflow detected error in your featureCount step usually indicates that the program is trying to write more data into memory …
Comment: gene Set with high AUC score but no cells assigned to cell type by eja.gssssse.r.m • 0
It sounds like your AUCell results may be showing high AUC scores without cell assignment due to thresholding or scoring cutoffs. Think of …
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Comment: Integration: Paired-end vs healthy single-end from a different source by igkryycpinmshzugby • 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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