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4.4k
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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
4.4k
views
Rhdf5lib install problems
R
bioconductor
rhdf5
biocmanager
3.5
5.4 years ago
cem45
• 0
0
votes
16
replies
4.3k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.5 years ago
writetoroopali
• 0
0
votes
11
replies
4.3k
views
Examples from keggList in KEGGREST don't all work
software error
keggrest
8.2 years ago
Bryan Hanson
• 0
0
votes
1
reply
4.3k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
5.9 years ago
Wolfgang Huber
★ 13k
3
votes
2
replies
4.3k
views
Automatic color assignment for annotations on ComplexHeatmap
complexheatmap
6.6 years ago
CodeAway
▴ 70
0
votes
31
replies
4.3k
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
1
reply
4.3k
views
biomaRt getLDS server error
biomaRt
Bioma
24 months ago
floriandeckert
▴ 30
0
votes
0
replies
4.3k
views
Du willst Heute noch realen Sex haben? ( Augen langen)
16.7 years ago
those1559@indiatimes.com
▴ 10
0
votes
0
replies
4.2k
views
Error in getClass(Class, where = topenv(parent.frame())) : "AnnotatedDataFrame" is not a defined class
Cancer
limma
Cancer
limma
15.3 years ago
Martin Morgan
25k
0
votes
0
replies
4.2k
views
LIMMA: plotMDS
limma
limma
11.9 years ago
Kripa R
▴ 180
5
votes
13
replies
4.2k
views
Getting error
enrichplot
clusterProfiler
org.Hs.eg.db
updated 2.1 years ago by
793345316
▴ 40 • written 2.1 years ago by
beslinail
• 0
0
votes
6
replies
4.1k
views
Error in getOneSeqFromBSgenomeMultipleSequences During singeR tutorial
error
4.8 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
2
votes
5
replies
4.1k
views
Merging multiple single cell experiment objects from different samples
sce
SingleCellExperiment
merge
updated 14 months ago by
mollyab12
• 0 • written 2.0 years ago by
achoppe
▴ 10
0
votes
2
replies
4.1k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt
AnnotationForge
23 months ago
Lan Anh
• 0
0
votes
0
replies
4.1k
views
Bioconductor 2.14 is released
BiocViews
aCGH
SNP
Sequencing
RNASeq
ChIPSeq
miRNA
Microarray
qPCR
Metabolomics
Coverage
10.0 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
4.0k
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
4.0k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
10.5 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
3
replies
4.0k
views
Plotting for mutational burden - R package
bioconductor
6.6 years ago
dt
▴ 20
1
vote
5
replies
4.0k
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 3.4 years ago by
Michael Lawrence
★ 11k • written 3.4 years ago by
Søren
• 0
0
votes
0
replies
4.0k
views
Limma for DNA methylation arrays?
Normalization
probe
limma
minfi
Normalization
probe
limma
minfi
10.4 years ago
Gustavo Fernández Bayón
▴ 440
2
votes
1
reply
3.9k
views
Unable to install DESeq2, 'getOption("repos") replaces Bioconductor standard repositories, see '?repositories' for details
BiocManager
updated 22 months ago by
Marcel Ramos
690 • written 22 months ago by
Yong
▴ 10
0
votes
2
replies
3.9k
views
Problem running featurecounts in Rsubread on GFF file
rsubread
featurecounts
gff
Grch38.p7 vs hg38
6.9 years ago
raf4
▴ 20
0
votes
1
reply
3.9k
views
SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
sva
sva
10.7 years ago
Ying Chen
▴ 110
2
votes
5
replies
3.9k
views
Warning in R
software error
8.9 years ago
Angel
▴ 40
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.4 years ago
Nader.Aryamanesh
• 0
0
votes
6
replies
3.9k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R
differential expression
rnaseqgene
8.5 years ago
JunLVI
▴ 40
0
votes
1
reply
3.9k
views
Processing Nanostring GeoMX Q3 normalized data as intensities with Limma
Limma
GeoMX
updated 2.7 years ago by
GeneEx
• 0 • written 2.8 years ago by
Matthew Thornton
▴ 350
1
vote
12
replies
3.8k
views
Problem with summarizeOverlaps function
genomicalignments
read counting
8.7 years ago
kgorczak
▴ 10
4
votes
3
replies
3.8k
views
subsetting GRanges object based on gene IDs
genomicranges
genomicfeatures
granges
subsetting
6.6 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
3.8k
views
ComBat
Transcription
Genetics
Pathways
Network
Survival
Cancer
Breast
Colon
Kidney
Leukemia
HIV
11.5 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
4.7 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 10 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
0
votes
2
replies
3.7k
views
wilcoxon signed rank test for data frame
wilcoxon signed rank test
data frame
affy
8.3 years ago
Smeeta Shrestha
▴ 20
16
votes
0
replies
3.7k
views
simultaneous use of robust and weighting methods in limma
limma
robust
arrayWeights
10.4 years ago • updated 7.9 years ago
Gordon Smyth
50k
0
votes
0
replies
3.7k
views
Interpretation of fold.changes for covariates in a linear model using voom
RNASeq
RNASeq
10.0 years ago
Gordon Smyth
50k
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.7 years ago
Gurkenkönig
▴ 10
7
votes
8
replies
3.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 5.3 years ago by
Bioconductor Community
0 • written 5.4 years ago by
michaelschoeber
▴ 20
0
votes
1
reply
3.7k
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 2.4 years ago by
arastoo
• 0
3
votes
0
replies
3.7k
views
biocLite() fails to install all limma dependencies from CRAN
Cancer
limma
Cancer
limma
17.0 years ago
Seth Falcon
★ 7.4k
1
vote
2
replies
3.7k
views
cnetplot with enrichKEGG results
clusterProfiler
enrichKEGG
cnetplot
2.4 years ago
fatimaruizdelabastida
• 0
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago
Deleted
▴ 70
0
votes
1
reply
3.7k
views
Subset VCF files using multiple criteria
vcf
variantannotation
granges
8.2 years ago
georgewwp
• 0
1
vote
0
replies
3.7k
views
Batch effect confounded with additional covariate
9.8 years ago
Guest User
★ 13k
1
vote
2
replies
3.6k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq
ChIPseeker
peak annotation
annotatePeak()
Diffbind
4.6 years ago
researcher
• 0
0
votes
4
replies
3.6k
views
DESeq2 installation in R
software error
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
wes
• 0
0
votes
1
reply
3.6k
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
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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