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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
14
votes
12
replies
9.4k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 7.8 years ago by
Steve Lianoglou
★ 13k • written 7.8 years ago by
CPR
▴ 30
14
votes
1
reply
2.0k
views
it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75
EnsDb.Hsapiens.v75
updated 3.4 years ago by
Batool
▴ 370 • written 3.4 years ago by
YunYun
▴ 70
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by
Juan Pablo
• 0 • written 8.4 years ago by
raya.fai
▴ 60
14
votes
19
replies
9.0k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 3.0 years ago by
Michael Love
42k • written 9.5 years ago by
andrew.j.skelton73
▴ 370
14
votes
10
replies
4.9k
views
HDF5 reading speed
rhdf5
hdf5
updated 6.3 years ago by
Mike Smith
★ 6.5k • written 6.3 years ago by
felicien.meunier
▴ 40
14
votes
21
replies
11k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation
shortread
dependency
updated 5.0 years ago by
January Weiner
▴ 240 • written 6.0 years ago by
joseph.elsherbini
▴ 60
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA
Hub Genes
KmE
Intramodular Connectivity
updated 8.9 years ago by
Peter Langfelder
★ 3.0k • written 8.9 years ago by
brohawndg
▴ 150
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma
differential gene expression
microarray
linear model
updated 8.9 years ago by
James W. MacDonald
66k • written 8.9 years ago by
bcbio_uk
▴ 10
14
votes
8
replies
2.7k
views
News:
Bioconductor packages now each have a DOI.
doi
citation
News
updated 6.7 years ago by
Martin Morgan
25k • written 6.8 years ago by
Sean Davis
21k
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
13
votes
10
replies
4.0k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger
deseq2
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
Matarit
• 0
13
votes
6
replies
6.3k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma
goana
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
carl.mann
▴ 20
13
votes
3
replies
12k
views
Understanding contrasts limma
limma
design and contrast matrix
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
Andy91
▴ 60
13
votes
12
replies
6.7k
views
From a ENST to ENSG
AnnotationDbi
3.3 years ago
suxxa
▴ 20
13
votes
2
replies
3.1k
views
voom with combat
limma
voom
combat
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
eldronzhou
▴ 10
13
votes
11
replies
12k
views
RNA-Seq, generate batch-free count matrix
edgeR
sva
updated 9.6 years ago by
Gordon Smyth
50k • written 9.8 years ago by
Brian Haas
▴ 90
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
2.0 years ago • updated 22 months ago
J-E
• 0
13
votes
11
replies
17k
views
edgeR TMM values
edger
8.3 years ago
ribioinfo
▴ 100
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 3 months ago by
Michael Love
42k • written 7.9 years ago by
adesrichard
▴ 30
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
jacorvar
▴ 40
13
votes
6
replies
7.1k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 8.4 years ago by
Michael Love
42k • written 8.4 years ago by
Stephen Turner
▴ 290
13
votes
16
replies
5.0k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR
deseq2
ase
allele
8.6 years ago
trianglescout
▴ 40
13
votes
2
replies
6.5k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma
covariate
continuous
categorical
adjustment
updated 8.8 years ago by
Gordon Smyth
50k • written 8.8 years ago by
sg45653
• 0
13
votes
5
replies
7.1k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 2.1 years ago by
Sarah
• 0 • written 7.9 years ago by
kaihami
▴ 30
13
votes
3
replies
3.5k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger
cpm
8.4 years ago
mikaelhc
▴ 20
13
votes
21
replies
6.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma
voom
hurdle
single cell
8.7 years ago
osa.zuta
▴ 40
13
votes
3
replies
2.2k
views
News:
Bioconductor teaching week
teaching
Carpentries
written 21 months ago by
Laurent Gatto
1.6k
13
votes
8
replies
16k
views
how to use biomaRt with ensembl build 37
biomaRt
ensembl
GRCh37
updated 9.6 years ago by
Thomas Maurel
▴ 800 • written 9.6 years ago by
Pablo marin-garcia
▴ 90
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.2 years ago by
alakatos
▴ 130 • written 9.2 years ago by
ycding
▴ 10
13
votes
35
replies
16k
views
RDAVIDWebService Error 301: Moved Permanently
rdavidwebservice
david
updated 5.8 years ago by
gevermalc
• 0 • written 8.9 years ago by
Vivek.b
▴ 100
13
votes
1
reply
2.9k
views
News:
Updated Bioconductor Package Submission Policy
package
submission
News
8.4 years ago
Martin Morgan
25k
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
abellonau
▴ 60
12
votes
7
replies
4.1k
views
illumina ht-12 v4 expression beadchip
microarray
illumina human ht-12 v4
updated 7.2 years ago by
Gordon Smyth
50k • written 7.3 years ago by
arisarkar88
▴ 40
12
votes
15
replies
3.5k
views
error with HDF5Array
hdf5array
biocparallel
updated 6.0 years ago by
Mike Smith
★ 6.5k • written 6.1 years ago by
cath
▴ 30
12
votes
8
replies
1.9k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 7.4 years ago by
Michael Love
42k • written 7.4 years ago by
Matthew McCall
▴ 830
12
votes
20
replies
2.1k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma
multifactorial design
design and contrast matrix
affymetrix microarrays
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
svlachavas
▴ 830
12
votes
3
replies
6.1k
views
Error while uploading Bioconductor packages - R Shiny
shiny
package
deploy
6.2 years ago
lloyd.izard
▴ 80
12
votes
4
replies
4.5k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.4 years ago by
Gordon Smyth
50k • written 7.0 years ago by
wd
▴ 30
12
votes
13
replies
7.8k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.7 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
elliott77
• 0
12
votes
7
replies
4.4k
views
Plot ggplot2 and ggbio Images Together
ggplot2
ggbio
cowplot
updated 4.8 years ago by
Assa Yeroslaviz
★ 1.5k • written 9.0 years ago by
andrew.j.skelton73
▴ 370
12
votes
2
replies
1.4k
views
`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore
EnsDb.Hsapiens.v75
TxDb.Hsapiens.UCSC.hg19.knownGene
3.4 years ago
Batool
▴ 370
12
votes
2
replies
4.6k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 9.4 years ago by
Simon Anders
★ 3.7k • written 9.4 years ago by
andrew.j.skelton73
▴ 370
12
votes
3
replies
4.9k
views
sva: how to incorporate adjusting variables
inveRsion
sva
inveRsion
sva
updated 10.7 years ago by
Jeff Leek
▴ 650 • written 10.7 years ago by
Meritxell Oliva
▴ 120
12
votes
11
replies
4.2k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply
biocparallel
deseq2
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
Lauren
▴ 40
12
votes
6
replies
21k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 9.0 years ago by
Michael Love
42k • written 9.0 years ago by
kmu004
▴ 50
12
votes
10
replies
6.6k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.2 years ago • updated 5.3 years ago
rached
▴ 60
12
votes
12
replies
2.1k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
apfelbapfel
▴ 30
12
votes
10
replies
6.5k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 9.0 years ago by
Aaron Lun
★ 28k • written 9.0 years ago by
Ryan C. Thompson
★ 7.9k
12
votes
6
replies
4.7k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind
Histone Chip-Seq
Summit size
updated 2.0 years ago by
Rory Stark
★ 5.2k • written 6.7 years ago by
urjaswita
▴ 40
1,000 results • Page
3 of 20
Recent ...
Replies
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
James W. MacDonald
66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
Brandon
• 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Kelly Street
• 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM
by
Vitor
• 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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