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12
votes
10
replies
6.6k
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Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva
gene set variation analysis
normalization
transformation
rna-seq
6.1 years ago • updated 5.3 years ago
rached
▴ 60
12
votes
2
replies
3.5k
views
How does edgeR compare to lme4?
rna-seq
edger
mixed model
random effects
lme4
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Ekarl2
▴ 80
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
5
replies
1.9k
views
News:
DOI for packages
DOI
doi
packages
citation
publication
News
6.6 years ago
shepherl
3.9k
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays
limma
differential gene expression
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Lennart.Vermander
▴ 10
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
12
votes
4
replies
3.9k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 5.5 years ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
maya.kappil
▴ 30
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
6
replies
3.4k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq
deseq2
edger
8.5 years ago
martiningi
▴ 40
12
votes
10
replies
6.5k
views
edgeR glmLRT with test="F"?
edger
dge
differential expression
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ryan C. Thompson
★ 7.9k
12
votes
13
replies
7.8k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.6 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
elliott77
• 0
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
6
replies
13k
views
makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
software error
maketxdbfrombiomart
updated 8.5 years ago by
Maciej Jończyk
• 0 • written 8.5 years ago by
luigi.cerulo
▴ 40
11
votes
23
replies
2.6k
views
crlmm support for Illumina arrays with no annotation package?
crlmm
QCarray
annotation
updated 4.4 years ago by
milo.yanez20
• 0 • written 4.6 years ago by
deanpett
▴ 30
11
votes
3
replies
4.9k
views
WGCNA - Signed vs signed hybrid networks
wgcna
updated 7.9 years ago by
Peter Langfelder
★ 3.0k • written 7.9 years ago by
bram.verstockt
▴ 20
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma
multifactorial design
diagnostic plots
affymetrix microarrays
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
svlachavas
▴ 830
11
votes
25
replies
11k
views
readCufflinks problem with extdata
cummerbund
updated 6.6 years ago by
markus.ball
▴ 10 • written 6.9 years ago by
biakemi
▴ 40
11
votes
8
replies
2.1k
views
Error when downloading data with recount3.
recount3
updated 2.1 years ago by
chris.wilks
▴ 70 • written 3.6 years ago by
Zach Brehm
▴ 20
11
votes
4
replies
1.8k
views
How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
bioconductor
cytogenetics
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
Arman Shahrisa
▴ 20
11
votes
3
replies
9.2k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
6.8 years ago • updated 3.5 years ago
tcalvo
▴ 90
11
votes
11
replies
15k
views
cannot install edgeR on M1 Mac
apple
m1
installation
silicon
updated 2.4 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Brian
▴ 90
11
votes
10
replies
9.5k
views
How to determine which edgeR glmFit and glmQLFit are better
edger
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
changjiang.h.xu
▴ 10
11
votes
18
replies
5.0k
views
What is the correct use of removeBatchEffect's design parameter
deseq2
limma
updated 3.2 years ago by
Gordon Smyth
50k • written 3.7 years ago by
Sam
▴ 10
11
votes
10
replies
4.2k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2
nanopore
5.0 years ago
David Eccles (gringer)
▴ 30
11
votes
17
replies
2.3k
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors
DataFrame
haven_labelled
haven
updated 17 months ago by
Danny Smith
▴ 20 • written 17 months ago by
Daniel E. Weeks
▴ 30
11
votes
6
replies
1.9k
views
edger glmQLFit mix glmLRT
edger
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Catalina Aguilar Hurtado
▴ 90
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 8.7 years ago by
Mark Cowley
▴ 400 • written 8.7 years ago by
willj
▴ 30
11
votes
9
replies
4.4k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
yi.huang
▴ 30
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
lirongrossmann
▴ 80
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.3 years ago
Yogender Gowtham
▴ 20
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.6 years ago
dietahanson
▴ 30
11
votes
15
replies
4.2k
views
Annotation for Affymetrix GeneChip PrimeView.
annotation
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
ammasakshay
• 0
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.3 years ago by
tleona3
• 0
11
votes
6
replies
3.8k
views
Log fold change on Limma
limma
multiple factor design
updated 8.9 years ago by
Steve Lianoglou
★ 13k • written 8.9 years ago by
ea1402
▴ 20
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 6.8 years ago by
Gordon Smyth
50k • written 15.5 years ago by
Daren Tan
▴ 190
11
votes
20
replies
4.2k
views
Detection p-value: difference between limma and lumi packages
p-value
detection
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
11
votes
0
replies
5.8k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
8.9 years ago
Martin Morgan
25k
11
votes
7
replies
17k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 2.5 years ago by
Michael Love
42k • written 8.2 years ago by
martin.hoelzer
▴ 20
11
votes
8
replies
4.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps
genomicalignments
updated 9.2 years ago by
Hervé Pagès
16k • written 9.2 years ago by
rxzlmn
▴ 10
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.8 years ago by
Robert Castelo
★ 3.3k • written 7.8 years ago by
rubi
▴ 110
11
votes
14
replies
11k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
kieran.mace
▴ 40
11
votes
1
reply
1.1k
views
News:
Rsubread now available for Windows
rsubread
News
4.7 years ago
Gordon Smyth
50k
11
votes
5
replies
4.0k
views
Scan error using biomart with version option
biomart
updated 6.3 years ago by
Mike Smith
★ 6.5k • written 6.4 years ago by
Chris Stubben
▴ 40
11
votes
4
replies
33k
views
DESeq2 baseMean counts
deseq2
updated 8.5 years ago by
Michael Love
42k • written 8.5 years ago by
zpingfeng
• 0
11
votes
0
replies
2.2k
views
News:
Bioconductor 3.0 is released!
news
News
9.6 years ago • updated 9.5 years ago
Dan Tenenbaum
★ 8.2k
11
votes
7
replies
6.4k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
kjo
▴ 70
11
votes
9
replies
1.6k
views
Correlation of a Linear Variable
limma
limma design matrix
updated 9.1 years ago by
James W. MacDonald
65k • written 9.1 years ago by
andrew.j.skelton73
▴ 370
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
Julie Zhu
★ 4.3k • written 5.3 years ago by
Gary
▴ 20
11
votes
8
replies
8.6k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 7.7 years ago by
Peter Langfelder
★ 3.0k • written 7.7 years ago by
gokce.ouz
▴ 70
11
votes
13
replies
4.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.5 years ago • updated 3.3 years ago
rohitsatyam102
▴ 20
45,667 results • Page
4 of 914
Recent ...
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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?
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…
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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