12
votes
33
replies
29k
views
Cannot install packages by BiocManager::install()
BiocManager
updated 2.1 years ago by 65k • written 3.0 years ago by ▴ 60
12
votes
4
replies
3.9k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.5 years ago by ★ 3.0k • written 5.5 years ago by ▴ 30
12
votes
3
replies
4.9k
views
sva: how to incorporate adjusting variables
inveRsion sva inveRsion sva
updated 10.7 years ago by ▴ 650 • written 10.7 years ago by ▴ 120
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
6.1 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 50k • written 7.9 years ago by ▴ 80
12
votes
2
replies
4.6k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 9.4 years ago by ★ 3.7k • written 9.4 years ago by ▴ 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 ★ 28k • written 7.0 years ago by ▴ 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 ★ 5.2k • written 6.7 years ago by ▴ 40
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
13
replies
7.8k
views
EdgeR Differential Expression analysis with NAs
EdgeR rnaseq NA
updated 9.6 years ago by ★ 28k • written 9.7 years ago by • 0
12
votes
6
replies
13k
views
makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
software error maketxdbfrombiomart
updated 8.5 years ago by • 0 • written 8.5 years ago by ▴ 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 • 0 • written 4.6 years ago by ▴ 30
11
votes
3
replies
4.9k
views
WGCNA - Signed vs signed hybrid networks
wgcna
updated 7.9 years ago by ★ 3.0k • written 7.9 years ago by ▴ 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 65k • written 8.7 years ago by ▴ 830
11
votes
25
replies
11k
views
readCufflinks problem with extdata
cummerbund
updated 6.6 years ago by ▴ 10 • written 6.9 years ago by ▴ 40
11
votes
8
replies
2.1k
views
Error when downloading data with recount3.
recount3
updated 2.1 years ago by ▴ 70 • written 3.6 years ago by ▴ 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 25k • written 6.6 years ago by ▴ 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 50k • written 2.9 years ago by ▴ 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 50k • written 8.4 years ago by ▴ 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 50k • written 3.7 years ago by ▴ 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 ▴ 20 • written 17 months ago by ▴ 30
11
votes
6
replies
1.9k
views
edger glmQLFit mix glmLRT
edger
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 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 ▴ 400 • written 8.7 years ago by ▴ 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 50k • written 7.8 years ago by ▴ 30
11
votes
8
replies
10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 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
15
replies
4.2k
views
Annotation for Affymetrix GeneChip PrimeView.
annotation
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.3 years ago by • 0
11
votes
6
replies
3.8k
views
Log fold change on Limma
limma multiple factor design
updated 8.9 years ago by ★ 13k • written 8.9 years ago by ▴ 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 50k • written 15.5 years ago by ▴ 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 50k • written 8.3 years ago by ▴ 150
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 42k • written 8.2 years ago by ▴ 20
11
votes
8
replies
4.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 10
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
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 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 42k • written 6.4 years ago by ▴ 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 ★ 6.5k • written 6.4 years ago by ▴ 40
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
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
11
votes
4
replies
33k
views
DESeq2 baseMean counts
deseq2
updated 8.5 years ago by 42k • written 8.5 years ago by • 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
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
8.6 years ago dietahanson ▴ 30
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 ★ 7.9k • written 7.9 years ago by ▴ 70
11
votes
9
replies
1.6k
views
Correlation of a Linear Variable
limma limma design matrix
updated 9.1 years ago by 65k • written 9.1 years ago by ▴ 370
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 ★ 3.0k • written 7.7 years ago by ▴ 70
45,666 results • Page 4 of 914
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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" …
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
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
India, 30 minutes ago
Greece, 50 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Poland, 1 hour ago
United States, 1 hour ago
Traffic: 430 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6