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Votes
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.7 years ago • updated 19 months ago
Michael Love
42k
32
votes
0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.7 years ago • updated 3.6 years ago
Gordon Smyth
50k
18
votes
4
replies
1.7k
views
`ggbio` package can't be loaded
ggbio
3.4 years ago
Batool
▴ 370
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
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
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
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
10
votes
8
replies
3.0k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
4.9 years ago
m93
▴ 10
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by
Daniel E. Weeks
▴ 30
8
votes
2
replies
3.0k
views
exprs function - clash with dplyr
exprs
dplyr
Biobase
6.0 years ago
Wolfgang Huber
★ 13k
8
votes
4
replies
6.9k
views
Can't upgrade to Bioconductor 3.3?
bioconductor
biocupgrade
upgrade
update
bioclite
8.0 years ago
enricoferrero
▴ 660
7
votes
9
replies
1.7k
views
codelink package is not installing
codelink
r
9.1 years ago
Agaz Hussain Wani
▴ 260
7
votes
8
replies
3.8k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 5.4 years ago by
Bioconductor Community
0 • written 5.5 years ago by
michaelschoeber
▴ 20
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.9 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.5 years ago by
Alexei Leliavski
▴ 60
7
votes
6
replies
2.0k
views
Help to find Volunteer who can review my bioconductor package before submission ?
r packages
submission
8.3 years ago
Jurat Shahidin
▴ 80
6
votes
6
replies
6.8k
views
Avoid upgrading BiocManager to 1.30.13; fix proposed
BiocManager
updated 2.8 years ago by
Mengfei
• 0 • written 3.0 years ago by
Vincent J. Carey, Jr.
6.7k
6
votes
3
replies
2.9k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq
differential exon usage
7.3 years ago
fizer
▴ 30
6
votes
3
replies
1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by
Darek
▴ 30
6
votes
0
replies
2.8k
views
BH vs BY in p.adjust + FDR interpretation
Coverage
limma
17.8 years ago • updated 8.3 years ago
Gordon Smyth
50k
6
votes
12
replies
1.8k
views
Error when loading DMRcate
DMRcate
15 months ago
Bazingastats
• 0
5
votes
1
reply
2.5k
views
fdrtool - correction of p-values - course found on huber.embl.de
fdrtool
p-value distribution
7.2 years ago
j.bergenstrahle
▴ 90
5
votes
3
replies
2.0k
views
ChIPQC error: "if (nrow(pv$binding) > 0) { : argument is of length zero"
chipqc
7.8 years ago
Danielle Denisko
▴ 30
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 4 months ago by
s.malik
• 0 • written 14 months ago by
jenniewoo
▴ 70
5
votes
5
replies
2.1k
views
SGE backend on Bioc AMI with Starcluster not recognising CPUs
ami
starcluster
biocparallel
sge
AWS
8.6 years ago
n.huckle
▴ 30
5
votes
4
replies
1.4k
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
6.0 years ago
slinker
▴ 20
5
votes
2
replies
693
views
outdated GEOmetadb.sqlite
GEOmetadb
15 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
5
votes
13
replies
4.3k
views
Getting error
enrichplot
clusterProfiler
org.Hs.eg.db
updated 2.2 years ago by
793345316
▴ 40 • written 2.2 years ago by
beslinail
• 0
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF
scater
3.6 years ago
lirongrossmann
▴ 40
5
votes
2
replies
1.2k
views
info(header(vcf)) remembers fields not imported: bugfix?
VariantAnnotation
7.8 years ago
kevin.rue
▴ 350
5
votes
3
replies
1.4k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
5.3 years ago
S.Webb6
▴ 40
5
votes
6
replies
2.5k
views
Download errors during Bioconductor 3.12 update
reactome.db
Bioconductor
BiocManager
updated 3.5 years ago by
Martin Morgan
25k • written 3.6 years ago by
Michael Steinbaugh
▴ 90
5
votes
5
replies
1.0k
views
Warning in In chromPeakSpectra: Lazy evaluation queue is not empty, results in NULL object
xcms
Spectra
updated 2.1 years ago by
Johannes Rainer
★ 2.0k • written 2.1 years ago by
e.terlova
▴ 20
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.6 years ago
khp
▴ 30
4
votes
15
replies
6.2k
views
mzR installation error: "unable to load shared object"
mzR
installation
8.8 years ago
Eugene
• 0
4
votes
9
replies
7.9k
views
Upper triangular matrix heatmap using pheatmap package
pheatmap
8.4 years ago
Deepak Tanwar
▴ 10
4
votes
2
replies
3.4k
views
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva
num.sv
6.9 years ago
brhead
▴ 40
4
votes
3
replies
3.9k
views
subsetting GRanges object based on gene IDs
genomicranges
genomicfeatures
granges
subsetting
6.7 years ago
Assa Yeroslaviz
★ 1.5k
4
votes
6
replies
1.6k
views
HTSeq command option for single-end reads
HTSeqGenie
21 months ago
Maryam.sed1400
• 0
4
votes
5
replies
1.7k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno
biomart
ensembl
8.3 years ago
igor
▴ 50
4
votes
4
replies
5.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
4
votes
7
replies
2.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
16 months ago • updated 15 months ago
Bernardo
▴ 10
4
votes
6
replies
4.7k
views
How to design formula in DESeq2 when setting blind=FALSE in rlog transformation?
deseq2
normalization
9.5 years ago
Xianjun Dong
▴ 10
4
votes
5
replies
2.5k
views
GDCprepare - error
TCGABiolinks
GDCprepare
4.8 years ago
vm
▴ 30
4
votes
0
replies
1.7k
views
how to test for genes of interest?
Normalization
Preprocessing
limma
Normalization
Preprocessing
limma
15.8 years ago
Gordon Smyth
50k
4
votes
5
replies
842
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
15 months ago
Robert Castelo
★ 3.3k
4
votes
2
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
3.0 years ago
aspangl1
▴ 30
4
votes
2
replies
668
views
A way to find which genome builds a package supports
build
genome
14 months ago
Dmitry
• 0
4
votes
4
replies
865
views
visualization problem with BioMM package
BioMM
3.9 years ago
parra.sev
▴ 20
4
votes
0
replies
2.3k
views
sva: No significant surrogate variables
Microarray
sva
Microarray
sva
11.2 years ago
Shraddha Pai
▴ 80
4
votes
4
replies
7.1k
views
what the test method for enrichGO in clusterProfiler?
clusterProfiler
2.4 years ago
xiaofeiwang18266
▴ 50
1,000 results • Page
1 of 20
Recent ...
Replies
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: 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?
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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