Showing : EDGER • reset
2
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1
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1.0k
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Error in `rownames<-`(`*tmp*`, value = list(genes
edger
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
5
votes
4
replies
1.9k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 10
2
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1
reply
1.1k
views
combine two differential expression methods
edger deseq2 dea publish
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
2
votes
4
replies
1.7k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 90
2
votes
1
reply
1.2k
views
edgeR normalisation which samples to include
edger normalization samples comparisons
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
0
votes
3
replies
1.8k
views
Differential expression of individual genes using edgeR
edger differential gene expression
8.1 years ago fawazfebin ▴ 60
26
votes
7
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13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 20
4
votes
9
replies
3.1k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ★ 2.0k
4
votes
2
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1.6k
views
Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
1
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2
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3.8k
views
DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
edgeR TCGA
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
4
votes
6
replies
2.2k
views
EdgeR: Replicate samples diverge in MDS plot
edger plotmds
8.1 years ago fawazfebin ▴ 60
3
votes
1
reply
2.5k
views
column nubering plotMDS
edger plotmds
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
10
votes
14
replies
5.9k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 90
10
votes
6
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5.5k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 8.1 years ago by ▴ 110 • written 10.4 years ago by 21k
0
votes
1
reply
916
views
differentially expressed genes form RSEM genes data
rnaseq edgeR
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 20
0
votes
3
replies
3.2k
views
topGO - missing value where TRUE/FALSE needed
topgo edger
8.2 years ago mictadlo ▴ 10
3
votes
3
replies
1.3k
views
Saving output from glmTreat to a csv file?
edger rna-seq
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
1
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1
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1.8k
views
Does edgeR accept decimal / integer read counts for differential expression ?
edger differential gene expression
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
8
votes
3
replies
2.6k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR rnaseq limma independent filtering
8.2 years ago Robert Castelo ★ 3.4k
0
votes
2
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2.0k
views
bias.data vector must have the same length as DEgenes vector!
edger goseq
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
3
votes
1
reply
685
views
adding genes to edgeR
edger
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
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3
replies
1.9k
views
goseq after edgeR
edger goseq
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
votes
2
replies
1.7k
views
how to build gene.pathway data.frame for non-model organism
limma kegg topgo dataframe edger
8.2 years ago mictadlo ▴ 10
2
votes
4
replies
1.7k
views
differentially expressed miRNA using edge R
edger
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 20
2
votes
2
replies
2.9k
views
plotMD plot change plot title
edger plotmd
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 10
0
votes
5
replies
3.4k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 10
3
votes
3
replies
1.1k
views
Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR) in M&M of biological paper
deseq2 edgeR
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 90
1
vote
2
replies
5.2k
views
Length of 'group' must equal number of columns in 'counts'
htseqcounts edger
updated 3.1 years ago by • 0 • written 8.2 years ago by ▴ 10
3
votes
7
replies
3.9k
views
read counts for each gene for edgeR
edger htseqcounts
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 10
2
votes
3
replies
3.7k
views
plotMDS axis labels for limma/EdgeR: PCA or PCoA
limma edgeR
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
2
votes
2
replies
1.2k
views
DESeq2 comparing differential expression results
deseq2 edger
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 70
11
votes
15
replies
3.8k
views
edgeR - MDS Plot for Count Data
edger DEG mds plot
8.2 years ago baus87 • 0
1
vote
2
replies
1.1k
views
normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
edgeR deseq2 normalization
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 670
1
vote
13
replies
3.4k
views
Why Differential expression results differ with edgeR and limma ?
limma edgeR differential gene expression r
8.2 years ago Biologist ▴ 120
2
votes
9
replies
2.4k
views
decideTests error with edgeR package
edger r differential gene expression
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 120
4
votes
4
replies
2.0k
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 7 months ago by • 0 • written 8.2 years ago by ▴ 370
3
votes
3
replies
8.8k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.2 years ago by 21k • written 8.2 years ago by ▴ 20
3
votes
1
reply
1.9k
views
Filtering step in Differential analysis with RSEM values
rsem differential gene expression edger
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 120
3
votes
1
reply
1.4k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
4
votes
8
replies
2.8k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger DGE no replicates
8.3 years ago • updated 8.2 years ago Stefany Solano • 0
1
vote
1
reply
1.7k
views
edgeR change first column to row name
edger tibble
updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
2
votes
14
replies
9.7k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.7 years ago by ▴ 20 • written 8.3 years ago by ▴ 120
1
vote
9
replies
2.4k
views
edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
edgeR differential gene expression
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 20
1
vote
1
reply
2.3k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma voom edgeR toptable output
updated 8.3 years ago by ★ 29k • written 8.3 years ago by ▴ 10
4
votes
8
replies
2.9k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR edger "glmqlftest()" timecourse model
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by ▴ 10
3
votes
11
replies
3.2k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by ▴ 10
0
votes
16
replies
2.5k
views
edgeR DE gene calculation problem
edgeR
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
1
vote
3
replies
2.3k
views
edgeR and lack of counts ID on CPM matrix
edgeR
8.3 years ago abrantes.patricia ▴ 10
1
vote
8
replies
2.2k
views
EdgeR model not of full rank
EdgeR rank model
8.3 years ago philip.freda • 0
2
votes
4
replies
1.4k
views
Adjusting for procedural effect
edger
8.3 years ago elineverbon ▴ 20
2,031 results • Page 19 of 41
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
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…
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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