Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
3
votes
3
replies
3.2k
views
Problem installing rhdf5
rhdf5
6.6 years ago
jariani.abb
▴ 10
3
votes
0
replies
2.2k
views
DESeq2 with data containing 3 factors or more and outlier detection
10.0 years ago
Michael Love
42k
3
votes
6
replies
1.9k
views
Integer overflow issue with ChIPQC
ChIPQC
Rstudio
updated 4.9 years ago by
Martin Morgan
25k • written 4.9 years ago by
Nitesh Kumar Singh
▴ 30
3
votes
0
replies
3.7k
views
biocLite() fails to install all limma dependencies from CRAN
Cancer
limma
Cancer
limma
17.1 years ago
Seth Falcon
★ 7.4k
3
votes
0
replies
2.8k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray
Normalization
Bayesian
Regression
Cancer
limma
Microarray
Normalization
Cancer
13.0 years ago
Richard Friedman
★ 2.0k
3
votes
3
replies
2.5k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth
R
salmon rna seq
salmon
6.5 years ago
Walter F. Baumann
▴ 10
3
votes
2
replies
1.1k
views
ASpli readCounts never ends!
aspli
readCounts
rna-seq
alternative splicing
AS
5.3 years ago
fernandalpcosta
▴ 10
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles
AnnotationForge
Bimap
GO
9.7 years ago
artur
▴ 80
3
votes
0
replies
1.6k
views
What's the correct way to normalize HTseq files with TCGAbiolinks
normalization
R
rnaseq
bioconductor
6.6 years ago
eshelden
▴ 40
3
votes
5
replies
2.1k
views
Volcano plot - select additional gene
EnhancedVolcano
RNASeqR
R
volcanoplot
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
camillab.
▴ 10
3
votes
1
reply
937
views
ChIPQC 'Contigs of interest are not all in Bam file!!' error
ChIPQC
3.0 years ago
Jonah
▴ 20
3
votes
0
replies
715
views
DSS : Different results between DMLtest and DMLtest.multifactor
DSS
2.7 years ago
cer.chloe
▴ 30
3
votes
1
reply
1.9k
views
TwoSampleMR and ieugwasr
ieugwasr
clumping
TwoSampleMR
updated 9 weeks ago by
zoheir.alayash
▴ 10 • written 2.2 years ago by
S T
▴ 90
3
votes
2
replies
968
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
2.1 years ago • updated 2.0 years ago
Dakarai
▴ 10
3
votes
3
replies
1.4k
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks
tcga
6.0 years ago
Benjamin Ostendorf
▴ 90
3
votes
3
replies
957
views
IHW: retain annotation columns in data when running `ihw(pvalue ~ covariate, data = ...)`
ihw
independent hypothesis weighting
4.1 years ago
david.laehnemann
▴ 10
3
votes
2
replies
4.4k
views
Automatic color assignment for annotations on ComplexHeatmap
complexheatmap
6.7 years ago
CodeAway
▴ 70
3
votes
9
replies
3.8k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.8 years ago
Gurkenkönig
▴ 10
3
votes
3
replies
3.3k
views
Modifying or writing a FCS file in R using the FlowCore package
FCS
flowframe
flowcore
flow cytometry
5.7 years ago
vonskopnik
▴ 10
3
votes
5
replies
1.2k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor
Install
library
biocmanager
updated 10 months ago by
Vincent J. Carey, Jr.
6.7k • written 10 months ago by
Ndimensional
▴ 20
3
votes
3
replies
1.8k
views
Error running CellMix SampleAnalysis vignette
software error
cellmix
vignette
expressionset
7.3 years ago
gabor.halasz
• 0
3
votes
3
replies
1.2k
views
I can't run PhyloProfile
AnnotationHubData
PhyloProfile
2.0 years ago
S.t
▴ 10
3
votes
4
replies
1.3k
views
Error in ChemmineR function propOB() and ChemmineOB prop_OB()
ChemmineR
ChemmineOB
updated 3.3 years ago by
Thomas Girke
★ 1.7k • written 3.4 years ago by
teresadijor
• 0
3
votes
1
reply
441
views
NPARC package y-variable
NPARC
NPA
updated 8 months ago by
nils.kurzawa
▴ 20 • written 8 months ago by
Aidan
• 0
3
votes
8
replies
26k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade
Rstudio
Bioconductor
R3.2.2
8.5 years ago
svlachavas
▴ 830
3
votes
8
replies
2.6k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData
AnnotationForge
2.1 years ago
Saber_J
▴ 10
3
votes
1
reply
805
views
Export from limma, edit, import to same class
limma
8.8 years ago
jjotto
• 0
3
votes
1
reply
2.4k
views
Problems installing Bioconductor -- pbkrtest
pbkrtest
8.4 years ago
codefused
▴ 30
3
votes
4
replies
1.5k
views
Can't install packages on R or via Bioconductor
R
installation
packages
annotatr
biocmanager
4.1 years ago
dakarai_esgdaille
▴ 10
3
votes
5
replies
1.5k
views
Error in installing multiClust package
package installation
8.2 years ago
Shamim Sarhadi
▴ 20
3
votes
4
replies
1.3k
views
Any way to detach or simplify nested GRangesList ?
grangeslist
filtering
r
7.7 years ago • updated 7.6 years ago
Jurat Shahidin
▴ 80
3
votes
2
replies
1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 2.5 years ago by
koushik
• 0 • written 7.3 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
4
replies
1.9k
views
Rhdf5lib Installation Problem - cp: cannot stat 'hdf5/c++/src/.libs/libhdf5_cpp.a'
software error
Rhdf5lib
5.0 years ago
z.navidi90
▴ 10
3
votes
4
replies
1.5k
views
GEOquery:Get error sampleNames
geoquery
updated 5.4 years ago by
Bioconductor Community
0 • written 5.5 years ago by
ustcxyf
▴ 10
3
votes
4
replies
2.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.7 years ago
franceschini.gianmarco
• 0
3
votes
4
replies
1.8k
views
Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments
MultiAssayExperiment
curatedTCGAData
TCGAutils
3.4 years ago
svlachavas
▴ 830
3
votes
9
replies
2.3k
views
problem for finding soft thresholding in WGCNA algorithm
wgcna
abline function
Scale independence diagram
5.6 years ago
modarzi
▴ 10
3
votes
6
replies
1.6k
views
error using org.Hs.eg.db package : Error in get(load(file)) :
org.hs.eg.db
select
9.1 years ago
tina.khajeh
• 0
3
votes
4
replies
2.2k
views
STRINGdb: Error in download.file(urlStr, temp)
STRINGdb
R
updated 2.3 years ago by
damian.szk
▴ 80 • written 2.5 years ago by
qardessio
▴ 10
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
3
votes
3
replies
656
views
RSS for new packages unavailable?
RSS
4.4 years ago
Malcolm Cook
★ 1.6k
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.8 years ago
94133
• 0
3
votes
2
replies
1.2k
views
DEXSeq analysis with large number of samples
dexseq
estimatedispersions
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
nemanja.vucic
▴ 10
3
votes
0
replies
502
views
Creating qPCRset for nondetects anlaysis from QuantStudio data
nondetects
qPCR
qPCRData
3.0 years ago
jhackett
▴ 30
3
votes
6
replies
1.1k
views
How to replace NAs values in "CompressedIntegerList" objects [reproducible example is included] ?
r
bug
granges
8.2 years ago
Jurat Shahidin
▴ 80
3
votes
0
replies
1.7k
views
An appeal to flow cytometry tools users
flow
flowcore
flowworkspace
cytometry
gating
7.3 years ago
Greg Finak
▴ 240
3
votes
3
replies
456
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 7 weeks ago by
alan.ocallaghan
▴ 160 • written 7 weeks ago by
Najla Abassi
• 0
3
votes
5
replies
2.5k
views
ChIPQC - can't read in bam files
chipqc
chipqcreport
5.7 years ago
molly_the_minotaur
▴ 30
3
votes
0
replies
1.7k
views
Interpret topGO reults
topGO
reults
8.9 years ago
megerdes
▴ 40
3
votes
8
replies
1.3k
views
please someone help me to run this code
software error
R
8.4 years ago
Angel
▴ 40
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
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!
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
Dario Strbenac
★ 1.5k
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
Locations
• All
Germany,
just now
Hong Kong,
18 minutes ago
UPF, Barcelona, Spain,
19 minutes ago
Israel,
19 minutes ago
Slovakia,
1 hour ago
Traffic: 383 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