11
votes
14
replies
22k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 17 months ago by • 0 • written 4.7 years ago by ▴ 40
11
votes
21
replies
5.1k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity
updated 5.3 years ago by ★ 4.3k • written 5.3 years ago by ▴ 20
11
votes
5
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7.4k
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 28 days ago by • 0 • written 9.2 years ago by ▴ 150
11
votes
15
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2.8k
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edgeR - MDS Plot for Count Data
edger DEG mds plot
6.7 years ago baus87 • 0
11
votes
1
reply
16k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 8.5 years ago by 42k • written 8.5 years ago by ▴ 20
10
votes
10
replies
1.7k
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RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
limma edger
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 10
10
votes
9
replies
3.9k
views
EdgeR Multifactorial design with batch effect-trouble with defining contrasts
edger design and contrast matrix multiple factor design multiple comparisons
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 20
10
votes
9
replies
1.7k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom voom limma rna-seq
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
10
votes
6
replies
3.7k
views
Coding vs Noncoding Genes in Hit List
biomaRt coding vs noncoding high throughput
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 30
10
votes
3
replies
3.1k
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News: Updates to BiocStyle formatting
BiocStyle vignettes rmarkdown latex News
6.8 years ago • updated 6.7 years ago Andrzej Oleś ▴ 750
10
votes
10
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7.0k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 9.2 years ago by 50k • written 9.2 years ago by • 0
10
votes
11
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2.4k
views
Counts from recount3 for DESeq2 analysis
recount3 DESeq2
updated 20 months ago by ★ 1.0k • written 2.1 years ago by ▴ 10
10
votes
1
reply
2.5k
views
How to explain how DESeq2 works to someone with zero bioinformatics background?
deseq2
updated 7.0 years ago by 42k • written 7.0 years ago by • 0
10
votes
6
replies
13k
views
DESEq2 VST error
deseq2 variancestabilizingtransformation
updated 21 months ago by • 0 • written 6.8 years ago by ▴ 60
10
votes
14
replies
8.6k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
7.8 years ago • updated 7.7 years ago anand_mt ▴ 90
10
votes
6
replies
5.4k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 90
10
votes
10
replies
3.8k
views
arrayQualityMetrics does not complete successfully
arrayqualitymetrics
updated 7.5 years ago by ▴ 10 • written 8.2 years ago by ▴ 10
10
votes
4
replies
13k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 30
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.2 years ago by ▴ 20 • written 8.3 years ago by ▴ 30
10
votes
2
replies
2.9k
views
How barcode-plot enrichment is calculated?
limma barcodeplot camera
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
10
votes
8
replies
2.2k
views
MA plot
MAplot
15 months ago Nathalie ▴ 20
10
votes
5
replies
2.3k
views
One replicate (one-color OR two-color) is enough to use Limma?
limma microarray
7.3 years ago kevin.m.hao ▴ 10
10
votes
8
replies
2.6k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 9.2 years ago by 16k • written 9.3 years ago by ▴ 40
10
votes
12
replies
2.9k
views
MultiAssayExperiment: how can i change name of a experiment in a multiassayexperiment object?
multiassayexperiment
updated 5.7 years ago by 700 • written 5.7 years ago by ▴ 160
10
votes
10
replies
7.4k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 8 weeks ago by • 0 • written 6 months ago by ▴ 10
10
votes
23
replies
13k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
2.8 years ago • updated 18 months ago soda ▴ 80
10
votes
7
replies
1.2k
views
Why in Bioconductor community people rarely upvote questions?
bioconductor
15 months ago • updated 14 months ago L ▴ 50
10
votes
6
replies
10k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 8.6 years ago by ▴ 650 • written 8.6 years ago by ▴ 110
10
votes
2
replies
1.3k
views
Possible to incorporate the sign or direction of an effect in the IHW covariate?
IHW
updated 8.1 years ago by ▴ 180 • written 8.1 years ago by ▴ 60
10
votes
10
replies
2.4k
views
Does package S4Vectors break ifelse?
S4Vectors ifelse
updated 6.9 years ago by ▴ 40 • written 8.8 years ago by ★ 3.0k
10
votes
5
replies
2.5k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 90
10
votes
15
replies
2.8k
views
News: BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
conference bioc2017 News
7.2 years ago • updated 6.8 years ago Martin Morgan 25k
10
votes
5
replies
6.2k
views
Error: This function only works when used with the ensembl BioMart.
biomart error
8.5 years ago anchel.gonzalez • 0
10
votes
8
replies
3.0k
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Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
4.9 years ago m93 ▴ 10
10
votes
8
replies
3.9k
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conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.9 years ago by ▴ 30
10
votes
0
replies
1.7k
views
News: European Bioconductor meeting 2017, 4 / 5 - 6 December, Cambridge, UK
news conference eurobioc2017 News
6.7 years ago • updated 6.5 years ago Aaron Lun ★ 28k
10
votes
4
replies
4.4k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
10
votes
14
replies
4.3k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
10
votes
18
replies
17k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
5.0 years ago Mozart ▴ 30
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 years ago by 16k • written 2.6 years ago by 42k
10
votes
7
replies
2.5k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 60
10
votes
11
replies
7.7k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 20
10
votes
1
reply
3.7k
views
WGCNA: Module preservation vs consensus analysis
WGCNA wgcna
updated 3.1 years ago by ▴ 70 • written 3.2 years ago by ▴ 60
10
votes
13
replies
3.7k
views
DE for genes with very low counts using limma.
limma voom limma-trend
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 180
10
votes
13
replies
4.3k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 8.9 years ago by • 0 • written 8.9 years ago by ▴ 10
10
votes
6
replies
4.7k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 6.7 years ago by ▴ 100 • written 8.9 years ago by 21k
10
votes
9
replies
1.8k
views
Overriding of shrinkage in DESeq2
deseq2
updated 8.1 years ago by 42k • written 8.1 years ago by ▴ 80
10
votes
0
replies
2.7k
views
News: Professor James Taylor
in memoriam News
4.1 years ago Martin Morgan 25k
10
votes
4
replies
2.1k
views
limma-trend with random effects and/or array weights
limma-trend duplicatecorrelation arrayweights limma
updated 6.6 years ago by 50k • written 6.7 years ago by ▴ 180
10
votes
10
replies
4.0k
views
Method for batch correction
combat sva limma
updated 8.1 years ago by ▴ 110 • written 8.1 years ago by ▴ 60
45,667 results • Page 5 of 914
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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