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6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 5 days ago
shepherl
3.8k
1
vote
5
replies
4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 2.8 years ago by
s.muroy
▴ 10
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 10 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
2
votes
7
replies
4.6k
views
Installing Local packages in Bioconductor
package
updated 8 months ago by
Boxun
• 0 • written 23 months ago by
BioC123
• 0
1
vote
7
replies
4.4k
views
Problems Installing biomaRt
biomaRt
updated 5 months ago by
James W. MacDonald
65k • written 2.1 years ago by
ksci
▴ 20
2
votes
28
replies
4.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
65k • written 16 months ago by
Manmohit
▴ 10
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.8 years ago by
stan
• 0
0
votes
4
replies
4.3k
views
SingleR Label.Ont
SingleR
updated 11 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.8 years ago by
seeker
• 0
0
votes
3
replies
4.2k
views
The MicrobiotaProcess package performed lefse analysis and had a problem drawing the tree
MicrobiotaProcess
offspring.tbl_tree_item
updated 9 months ago by
Itscontentstop
• 0 • written 9 months ago by
fengjieli2021
• 0
2
votes
2
replies
4.1k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation
rlog transformation
deseq2
updated 5 months ago by
Alessandro Silvestris
• 0 • written 6.4 years ago by
lirongrossmann
▴ 80
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by
James W. MacDonald
65k • written 7.8 years ago by
szenitha
▴ 20
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 6 months ago by
Marcel Ramos
690 • written 20 months ago by
Recep
▴ 20
2
votes
2
replies
3.9k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by
Trinh
• 0 • written 7.8 years ago by
mdtorohernando
▴ 10
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 6 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.1 years ago by
panagiotis.mokos
▴ 40
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 3 months ago by
Mingkee
• 0 • written 6.8 years ago by
yura.grabovska
▴ 30
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.5 years ago by
tanyabioinfo
▴ 20
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
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 5 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 7 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate
minfi
updated 12 weeks ago by
Tim Peters
▴ 170 • written 7.1 years ago by
Jenny Drnevich
★ 2.0k
0
votes
4
replies
3.6k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 10 months ago by
Marco
• 0 • written 4.4 years ago by
mathai.c
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
1
vote
4
replies
3.5k
views
ggtree functions suddenly stopped working: "Error in offspring.tbl_tree_item(..."
ggtree
updated 9 months ago by
xushuangbin
• 0 • written 9 months ago by
Hank
• 0
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 3 months ago by
YNPAN910
• 0 • written 4.7 years ago by
maya.kappil
▴ 30
1
vote
11
replies
3.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by
Manuel
• 0 • written 10 months ago by
Elham
• 0
0
votes
1
reply
3.4k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Aytaç
• 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.2 years ago by
changxu.fan
▴ 20
1
vote
3
replies
3.3k
views
SRAdb: Error downloading sqlite files
sradb
written 6.5 years ago by
arielle
• 0
0
votes
3
replies
3.3k
views
ASpli: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': 'start' or 'end' canno…
ASpli
updated 7 months ago by
andresrabinovich
• 0 • written 18 months ago by
thithusuong.nguyen
• 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 6 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
2
votes
10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by
Michael Love
41k • written 5.7 years ago by
andrebolerbarros
▴ 20
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 3 months ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
written 3.3 years ago by
Carolina
• 0
2
votes
9
replies
3.1k
views
NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 5 months ago by
IP
• 0 • written 20 months ago by
KMS
▴ 20
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 25 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.1 years ago by
src3
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 21 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
0
votes
4
replies
3.1k
views
Problems with FLOWAI
flowAI
written 3.0 years ago by
msoares
• 0
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by
pbachali
▴ 50
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 5 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
0
votes
5
replies
3.0k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by
adi.rotem
• 0 • written 8.0 years ago by
dsg16
▴ 20
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 3 months ago by
Matthias Lienhard
▴ 240 • written 7.1 years ago by
justinburgener
▴ 20
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
1,734 results • Page
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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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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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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