6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 10 days ago shepherl 3.9k
1
vote
5
replies
4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 9 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
3
votes
3
replies
4.7k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
2
votes
7
replies
4.6k
views
Installing Local packages in Bioconductor
package
updated 8 months ago by • 0 • written 24 months ago by • 0
1
vote
7
replies
4.4k
views
Problems Installing biomaRt
biomaRt
updated 5 months ago by 65k • written 2.1 years ago by ▴ 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 65k • written 17 months ago by ▴ 10
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 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 • 0 • written 9 months ago by • 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 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 • 0 • written 6.4 years ago by ▴ 80
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 20 months ago by ▴ 20
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by 65k • written 7.8 years ago by ▴ 20
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 7 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
votes
2
replies
4.0k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 9 months ago by • 0 • written 7.8 years ago by ▴ 10
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.8 years ago by ▴ 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 • 0 • written 3.1 years ago by ▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 11 weeks ago by 50k • written 4.8 years ago by • 0
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.5 years ago by ▴ 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 • 0 • written 3.2 years ago by • 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 3 months ago by ▴ 170 • written 7.1 years ago by ★ 2.0k
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 6 weeks ago by • 0 • written 6.4 years ago by ▴ 20
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 • 0 • written 4.4 years ago by • 0
1
vote
4
replies
3.5k
views
ggtree functions suddenly stopped working: "Error in offspring.tbl_tree_item(..."
ggtree
updated 9 months ago by • 0 • written 9 months ago by • 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 ▴ 80
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 3 months ago by • 0 • written 4.7 years ago by ▴ 30
0
votes
1
reply
3.5k
views
Bioconductor version cannot be validated
Bioconductor Annotation Ann
updated 7 months ago by 65k • written 7 months ago by • 0
1
vote
11
replies
3.5k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by • 0 • written 10 months ago by • 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 ▴ 20
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 • 0 • written 6.6 years ago by • 0
0
votes
3
replies
3.4k
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 • 0 • written 18 months ago by • 0
1
vote
3
replies
3.3k
views
SRAdb: Error downloading sqlite files
sradb
written 6.5 years ago by • 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by • 0 • written 17 months ago by • 0
2
votes
10
replies
3.2k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 6 months ago by 41k • written 5.7 years ago by ▴ 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 ▴ 10 • written 8.4 years ago by ▴ 10
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
2
votes
9
replies
3.1k
views
NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 5 months ago by • 0 • written 20 months ago by ▴ 20
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 4 weeks ago by 50k • written 9.8 years ago by ▴ 40
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 26 days ago by ▴ 10 • written 2.0 years ago by • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.2 years ago by • 0
0
votes
4
replies
3.1k
views
Problems with FLOWAI
flowAI
written 3.0 years ago by • 0
2
votes
3
replies
3.1k
views
Filtering low intensity probes in microarray data
Hugene1.0 ST
written 6.8 years ago by ▴ 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 6 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
0
votes
5
replies
3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 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 ▴ 60
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
1
vote
9
replies
2.9k
views
DEGreport installation help
DEGreport
updated 8 months ago by 65k • written 19 months ago by ▴ 20
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
1,000 results • Page 2 of 20
Recent ...
Replies
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards • All
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.8k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Locations • All
United States, just now
United Kingdom, 7 minutes ago
France, 15 minutes ago
United States, 15 minutes ago
United States, 17 minutes ago
Traffic: 708 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