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Views
Votes
18
votes
4
replies
1.7k
views
`ggbio` package can't be loaded
ggbio
3.4 years ago
Batool
▴ 370
18
votes
3
replies
2.9k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma
voomwithqualityweights
gene set analysis
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
BharathAnanth
▴ 80
18
votes
12
replies
3.8k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 8.9 years ago by
Michael Love
42k • written 8.9 years ago by
Ryan C. Thompson
★ 7.9k
18
votes
18
replies
4.8k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma
batch effect
ComBat
differential gene expression
updated 8.6 years ago by
W. Evan Johnson
▴ 850 • written 8.6 years ago by
svlachavas
▴ 830
18
votes
10
replies
7.1k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger
estimatedispersions
glm
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
maltethodberg
▴ 180
17
votes
7
replies
12k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2
ensembl
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
casey.rimland
▴ 150
17
votes
7
replies
6.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 8.0 years ago by
Ryan C. Thompson
★ 7.9k • written 8.0 years ago by
ompandey
▴ 10
17
votes
8
replies
3.2k
views
How to check the read length for all the TCGA data samples in GDC?
gdc
tcga
wes
gdc data
updated 6.1 years ago by
Sean Davis
21k • written 6.1 years ago by
Biologist
▴ 110
17
votes
5
replies
4.1k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
mdoering
▴ 20
17
votes
4
replies
9.0k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 7 weeks ago by
Mj.A.
• 0 • written 5.3 years ago by
shepherl
3.9k
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by
Leanne
• 0 • written 13.6 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
17
votes
5
replies
4.9k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.1 years ago
AS
▴ 70
17
votes
4
replies
16k
views
How to properly sort GRanges?
granges
genomicranges
sort
seqnames
order
updated 9.1 years ago by
yinghua
▴ 30 • written 9.5 years ago by
enricoferrero
▴ 660
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Pauly Lin
▴ 150
17
votes
9
replies
33k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 3.3 years ago by
Michael Love
42k • written 8.3 years ago by
ribioinfo
▴ 100
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
Anke Busch
▴ 10
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 23 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
17
votes
4
replies
33k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.7 years ago by
Ram
▴ 210 • written 3.7 years ago by
c.e.chong
▴ 10
16
votes
5
replies
7.5k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
komal.rathi
▴ 120
16
votes
9
replies
6.6k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 8.2 years ago by
florian.noack
▴ 60
16
votes
4
replies
11k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 8.6 years ago by
Michael Lawrence
★ 11k • written 8.6 years ago by
khauser130d
▴ 50
16
votes
13
replies
4.4k
views
Camera and ROAST
limma
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
Nuno Pires
▴ 30
16
votes
0
replies
3.8k
views
simultaneous use of robust and weighting methods in limma
limma
robust
arrayWeights
10.4 years ago • updated 8.0 years ago
Gordon Smyth
50k
16
votes
6
replies
3.3k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 7.8 years ago by
Charity Law
▴ 90 • written 7.8 years ago by
maltethodberg
▴ 180
16
votes
40
replies
8.7k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.4 years ago by
Clara
• 0 • written 4.8 years ago by
lim6432
▴ 50
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
16
votes
5
replies
14k
views
Error: Bioconductor version '3.8' requires R version '3.5'
software error
updated 5.0 years ago by
Mike Smith
★ 6.5k • written 5.0 years ago by
romanowska.j
▴ 10
16
votes
13
replies
16k
views
deseq2 normalized data with heatmap
deseq2
updated 2.9 years ago by
Ian
▴ 10 • written 3.7 years ago by
linouhao
▴ 20
16
votes
10
replies
6.7k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 15 months ago by
Hervé Pagès
16k • written 2.6 years ago by
sarah.howles
▴ 20
16
votes
12
replies
2.4k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
2.1 years ago
Joan Miró
▴ 80
15
votes
2
replies
18k
views
Extract sequence from DNAStringSet object
dnastringset
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
komal.rathi
▴ 120
15
votes
9
replies
13k
views
Best way to convert uniprot accessions to entrez gene identifiers in R
org.hs.eg.db
uniprot accessions
entrez gene identifiers
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
Aditya
▴ 160
15
votes
4
replies
2.8k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
WouterDeCoster
▴ 130
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
28 days ago • updated 17 days ago
Chris
▴ 10
15
votes
6
replies
29k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 5.9 years ago by
ftroot1010
▴ 20 • written 6.1 years ago by
jxb.dev
▴ 40
15
votes
12
replies
66k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 9.2 years ago by
Steve Lianoglou
★ 13k • written 9.2 years ago by
john
▴ 120
15
votes
3
replies
1.6k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 2.3 years ago by
molly_the_minotaur
▴ 30 • written 3.5 years ago by
bi.mi
▴ 90
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.5 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.7 years ago by
jol.espinoz
▴ 40
15
votes
13
replies
3.1k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 2.5 years ago by
xiang
▴ 10 • written 2.5 years ago by
immuno.dh
▴ 20
15
votes
18
replies
3.4k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
Raito92
▴ 60
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago
Chris
▴ 10
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma
microarray
updated 9.3 years ago by
Sean Davis
21k • written 9.3 years ago by
Andreas Heider
▴ 340
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges
grangeslist
granges
s4
updated 2.1 years ago by
Hervé Pagès
16k • written 7.9 years ago by
richierocks
▴ 40
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
9.5 years ago
salahm
▴ 70
15
votes
12
replies
2.5k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2
ZINB-WaVE
single cell
RNA-seq
differential expression
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
rory.kirchner
▴ 60
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.5 years ago
Deleted
▴ 70
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
8.0 years ago • updated 7.9 years ago
giroudpaul
▴ 40
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 2.3 years ago by
Nadine
▴ 60 • written 9.6 years ago by
Darya Vanichkina
▴ 120
14
votes
4
replies
29k
views
heatmap.2() get matrix after hierarchical clustering
Clustering
Clustering
updated 11.6 years ago by
Thomas Girke
★ 1.7k • written 11.6 years ago by
Guest User
★ 13k
14
votes
9
replies
15k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
9.4 years ago
gavrielmatt
▴ 30
45,668 results • Page
2 of 914
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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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