Showing : edgeR • reset
0
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2.2k
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Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 130
3
votes
5
replies
1.7k
views
edgeR trended or tagwise
edger glmqlftest()
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 60
2
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5
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4.5k
views
Analyse only protein_coding genes
bioconductor edger rna-seq
7.9 years ago martin.weihrauch ▴ 20
2
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3
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2.0k
views
Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
7.9 years ago r.aprianto ▴ 30
9
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6
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2.5k
views
Representative gene expression value in one condition with several replicates
rnaseq gene expression edger
updated 7.9 years ago by 53k • written 7.9 years ago by ▴ 20
2
votes
2
replies
2.8k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 2.2 years ago by • 0 • written 7.9 years ago by • 0
3
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7
replies
7.2k
views
Limma PlotMDS: what values should be used?
limma edger plotmds tmm masigpro
7.9 years ago dacaba.92 ▴ 10
2
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4
replies
1.6k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by • 0
1
vote
5
replies
8.4k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 7.9 years ago by ▴ 20 • written 7.9 years ago by • 0
2
votes
1
reply
1.4k
views
Edge R 3.16.5 Installation pathway issues/unable to update required packages
run_edger edger
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
3
votes
9
replies
10k
views
edgeR and batch effect
edger
updated 8.0 years ago by • 0 • written 8.5 years ago by ▴ 10
0
votes
5
replies
2.0k
views
glmTreat Errors for multi coefficient and analysis of deviance situations.
edgeR glmTreat analysis of deviance
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by ▴ 80
0
votes
5
replies
2.2k
views
normalization of CHIP-seq samples (ChIP and INPUT)
edgeR deseq2 voom limma
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 670
6
votes
6
replies
9.3k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
8.0 years ago Denniswu ▴ 20
2
votes
9
replies
2.4k
views
Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
8.0 years ago David R ▴ 90
2
votes
2
replies
977
views
Outdated packages in R 3.4.2
limma edgeR
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
3
votes
3
replies
4.5k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger DGEList org.hs.eg.db gene annotation
updated 4.1 years ago by • 0 • written 8.0 years ago by ▴ 840
3
votes
2
replies
3.5k
views
Can't install edgeR because of compilation error: make: *** [R_add_prior_count.o] Error 1
edger compilation error
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
1
vote
1
reply
2.9k
views
limma voom's (and edger's) use of scaling factors
limma limma voom normalization edger
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 10
0
votes
8
replies
2.3k
views
edgeR: multi-subject time series analysis
timecourse multiple groups edgeR
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 80
0
votes
0
replies
1.7k
views
Specific considerations in RNA-Seq DE analysis with edgeR pipeline for a TCGA dataset starting with HTSeq counts
edgeR rnaseq DEanalysis TCGA independent filtering
8.0 years ago svlachavas ▴ 840
1
vote
2
replies
1.0k
views
normalization of ChIP-seq
limma edgeR deseq2
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by ▴ 670
5
votes
2
replies
1.8k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma edger voom voomWithQualityWeights limma-voom
updated 8.0 years ago by 53k • written 8.0 years ago by ★ 4.1k
5
votes
9
replies
3.9k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 2.2 years ago by • 0 • written 8.0 years ago by ▴ 10
4
votes
3
replies
1.6k
views
RNASeq interaction between factors with edgeR when cpms tend to zero
rnaseq edgeR edger main and interaction effects
8.0 years ago David R ▴ 90
1
vote
7
replies
2.0k
views
Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 20
1
vote
2
replies
2.2k
views
DGE analysis with TMM and gene length normalized data.
edger deseq2 tmm normalised values
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
0
votes
4
replies
2.9k
views
Adaptation of DESeq/edgeR model for CRISPR drop-out screen
crispr edger deseq deseq2
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
0
votes
3
replies
1.6k
views
Adding gene names which are differentially expressed in the plot
edgeR plot differential gene expression
8.0 years ago fawazfebin ▴ 60
3
votes
2
replies
5.3k
views
No genes found in universe : goana error
edger goana gene ontology
8.1 years ago • updated 8.0 years ago fawazfebin ▴ 60
4
votes
5
replies
2.1k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
8.1 years ago • updated 8.0 years ago fawazfebin ▴ 60
16
votes
12
replies
9.2k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 14 months ago by • 0 • written 9.7 years ago by ▴ 60
2
votes
4
replies
1.6k
views
edgeR - problem with glmQLFTest()
edger
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
0
votes
3
replies
2.5k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger DGE coef
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
0
votes
1
reply
1.4k
views
Running model separately for each cell line or as the same model?
limma deseq2 edger rnaseq
updated 8.1 years ago by ▴ 120 • written 8.1 years ago by ▴ 60
2
votes
1
reply
8.7k
views
edgeR: PValue, adjusted PValue, FDR
edger
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 20
6
votes
6
replies
13k
views
Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
rnaseq edger
8.1 years ago Jack ▴ 20
4
votes
8
replies
2.2k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 20
4
votes
11
replies
5.7k
views
edgeR cpm filter
edger independent filtering multiple factor design cpm
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
0
votes
2
replies
1.5k
views
gene names disapper from heatmap.2 after adding gene descripton
heatmap.2 edger
8.1 years ago mictadlo ▴ 10
4
votes
4
replies
6.1k
views
Error in plot.new() : figure margins too large
edger
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 10
3
votes
4
replies
5.2k
views
saving a plot as png and also showing inside Rstudio
edger ggplot2
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
7
votes
2
replies
7.5k
views
How is it possible to get a legend outside plotMDS?
edger ggplot2
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 10
3
votes
9
replies
2.4k
views
edgeR long vectors support when normalizing abundance matrix
edger cpm
8.1 years ago jtremblay514 • 0
0
votes
2
replies
1.8k
views
creating design and count matrix for rna-seq differential expression
limma rnaseq edger
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
2
votes
1
reply
1.5k
views
How to filter glmTreat results by a false discovery rate (FDR) of 0.05
edger
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
0
votes
1
reply
24k
views
Error in .External.graphics(C_layout, num.rows, num.cols, mat, as.integer(num.figures)
edger ggplot
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
2
votes
3
replies
1.2k
views
adding a description column to glmTreat output
edger
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 10
2
votes
1
reply
2.3k
views
Error in plot.new() : figure margins too large
edger ggplot
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 10
2
votes
8
replies
1.7k
views
Using multiple factor analysis in edgeR
edger
8.1 years ago Mahnaz Kiani ▴ 20
2,031 results • Page 18 of 41
Recent ...
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Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by Kevin Blighe ★ 4.0k
Hello Lei, The concept of pseudobulk analysis applies equally to cell surface protein data as it does to gene expression data in single-…
Answer: Corrupted SQLite while trying to install PANTHER.db? by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error message indicates that the SQLite database within the PANTH…
Answer: Corrupted SQLite while trying to install PANTHER.db? by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. Hello Alan. The error message "database disk image is malformed" i…
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Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
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