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4.5k
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Phyloseq: How to add sample table to phyloseq object
phyloseq
sample_table
phyloseq
9.3 years ago
Brian Smith
▴ 120
0
votes
3
replies
4.5k
views
Rhdf5lib install problems
R
bioconductor
rhdf5
biocmanager
3.5
5.5 years ago
cem45
• 0
0
votes
11
replies
4.4k
views
Examples from keggList in KEGGREST don't all work
software error
keggrest
8.2 years ago
Bryan Hanson
• 0
0
votes
16
replies
4.4k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.6 years ago
writetoroopali
• 0
0
votes
0
replies
4.4k
views
Du willst Heute noch realen Sex haben? ( Augen langen)
16.8 years ago
those1559@indiatimes.com
▴ 10
0
votes
1
reply
4.4k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
6.0 years ago
Wolfgang Huber
★ 13k
3
votes
2
replies
4.4k
views
Automatic color assignment for annotations on ComplexHeatmap
complexheatmap
6.7 years ago
CodeAway
▴ 70
0
votes
1
reply
4.4k
views
biomaRt getLDS server error
biomaRt
Bioma
2.0 years ago
floriandeckert
▴ 30
0
votes
31
replies
4.4k
views
Error in find DEXSeq package
deseq
dexseq
9.0 years ago
engr.yahya602
• 0
1
vote
3
replies
4.3k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation
permission denied
RTCGAToolbox
TCGAbiolinks
4.0 years ago
julia.tutzauer
• 0
0
votes
0
replies
4.3k
views
Error in getClass(Class, where = topenv(parent.frame())) : "AnnotatedDataFrame" is not a defined class
Cancer
limma
Cancer
limma
15.4 years ago
Martin Morgan
25k
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
0
votes
0
replies
4.3k
views
LIMMA: plotMDS
limma
limma
12.0 years ago
Kripa R
▴ 180
2
votes
5
replies
4.2k
views
Merging multiple single cell experiment objects from different samples
sce
SingleCellExperiment
merge
updated 14 months ago by
mollyab12
• 0 • written 2.1 years ago by
achoppe
▴ 10
0
votes
6
replies
4.2k
views
Error in getOneSeqFromBSgenomeMultipleSequences During singeR tutorial
error
4.9 years ago
dfcarril
• 0
0
votes
2
replies
4.1k
views
biocLite() upgrade issue when same package in 2 libraries
biocinstaller
8.8 years ago
Jenny Drnevich
★ 2.0k
0
votes
2
replies
4.1k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt
AnnotationForge
24 months ago
Lan Anh
• 0
0
votes
0
replies
4.1k
views
cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing
miRNA
edgeR
Sequencing
miRNA
edgeR
9.9 years ago
Gordon Smyth
50k
0
votes
0
replies
4.1k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
10.6 years ago
Dan Tenenbaum
★ 8.2k
1
vote
5
replies
4.1k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw
rtracklayer
http
RStudio
updated 3.5 years ago by
Michael Lawrence
★ 11k • written 3.5 years ago by
Søren
• 0
0
votes
0
replies
4.1k
views
Bioconductor 2.14 is released
BiocViews
aCGH
SNP
Sequencing
RNASeq
ChIPSeq
miRNA
Microarray
qPCR
Metabolomics
Coverage
10.1 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
4.0k
views
[R] object is not subsettable
GO
Cancer
annotate
GO
Cancer
annotate
17.2 years ago
Seth Falcon
★ 7.4k
2
votes
1
reply
4.0k
views
Unable to install DESeq2, 'getOption("repos") replaces Bioconductor standard repositories, see '?repositories' for details
BiocManager
updated 23 months ago by
Marcel Ramos
700 • written 23 months ago by
Yong
▴ 10
2
votes
3
replies
4.0k
views
Plotting for mutational burden - R package
bioconductor
6.6 years ago
dt
▴ 20
0
votes
0
replies
4.0k
views
Limma for DNA methylation arrays?
Normalization
probe
limma
minfi
Normalization
probe
limma
minfi
10.5 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
1
reply
4.0k
views
SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
sva
sva
10.8 years ago
Ying Chen
▴ 110
0
votes
1
reply
3.9k
views
Processing Nanostring GeoMX Q3 normalized data as intensities with Limma
Limma
GeoMX
updated 2.8 years ago by
GeneEx
• 0 • written 2.9 years ago by
Matthew Thornton
▴ 360
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.4 years ago
Nader.Aryamanesh
• 0
0
votes
2
replies
3.9k
views
Problem running featurecounts in Rsubread on GFF file
rsubread
featurecounts
gff
Grch38.p7 vs hg38
7.0 years ago
raf4
▴ 20
2
votes
5
replies
3.9k
views
Warning in R
software error
9.0 years ago
Angel
▴ 40
0
votes
6
replies
3.9k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R
differential expression
rnaseqgene
8.6 years ago
JunLVI
▴ 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
1
vote
12
replies
3.9k
views
Problem with summarizeOverlaps function
genomicalignments
read counting
8.7 years ago
kgorczak
▴ 10
0
votes
0
replies
3.9k
views
ComBat
Transcription
Genetics
Pathways
Network
Survival
Cancer
Breast
Colon
Kidney
Leukemia
HIV
11.6 years ago
SSc Array Core
▴ 10
1
vote
5
replies
3.8k
views
how to get normalized count data from edgeR using TMM methods
edger
normalization
4.8 years ago
15958021290
▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 3 months ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
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
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
0
votes
1
reply
3.8k
views
An error has occurred! Navigation containers expect a collection of `bslib::nav()`/`shiny::tabPanel()`s and/or `bslib::nav_menu()`/`shiny::navbarMenu…
FastqCleaner
updated 2.2 years ago by
Jaisri
• 0 • written 2.5 years ago by
arastoo
• 0
0
votes
0
replies
3.8k
views
Interpretation of fold.changes for covariates in a linear model using voom
RNASeq
RNASeq
10.1 years ago
Gordon Smyth
50k
3
votes
9
replies
3.8k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.8 years ago
Gurkenkönig
▴ 10
0
votes
2
replies
3.8k
views
wilcoxon signed rank test for data frame
wilcoxon signed rank test
data frame
affy
8.3 years ago
Smeeta Shrestha
▴ 20
1
vote
2
replies
3.7k
views
cnetplot with enrichKEGG results
clusterProfiler
enrichKEGG
cnetplot
2.5 years ago
fatimaruizdelabastida
• 0
0
votes
4
replies
3.7k
views
DESeq2 installation in R
software error
updated 3.7 years ago by
Martin Morgan
25k • written 3.7 years ago by
wes
• 0
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
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.5 years ago
Deleted
▴ 70
0
votes
3
replies
3.7k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler
enrichplot
clusterpro
doseR
dose
updated 22 months ago by
Guido Hooiveld
★ 4.0k • written 22 months ago by
rama
▴ 10
0
votes
1
reply
3.7k
views
Subset VCF files using multiple criteria
vcf
variantannotation
granges
8.3 years ago
georgewwp
• 0
1
vote
2
replies
3.7k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq
ChIPseeker
peak annotation
annotatePeak()
Diffbind
4.7 years ago
researcher
• 0
1
vote
0
replies
3.7k
views
Batch effect confounded with additional covariate
9.8 years ago
Guest User
★ 13k
1,000 results • Page
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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!
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…
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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