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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
0
replies
4.4k
views
Du willst Heute noch realen Sex haben? ( Augen langen)
16.8 years ago
those1559@indiatimes.com
▴ 10
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
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
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
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
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
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.4 years ago
Nader.Aryamanesh
• 0
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
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
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
3
votes
9
replies
3.8k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.8 years ago
Gurkenkönig
▴ 10
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
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
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
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
0
votes
1
reply
3.7k
views
ape - delete bootstrap values (node.labels) less than a certain value
ape
bootstrap
node
phylogenetic
tree
8.9 years ago
wd
▴ 30
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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