3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 3 months ago by ★ 4.0k • written 3.3 years ago by • 0
2
votes
7
replies
4.8k
views
Installing Local packages in Bioconductor
package
updated 9 months ago by • 0 • written 2.0 years ago by • 0
3
votes
3
replies
4.8k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 11 months ago by ★ 4.0k • written 4.1 years ago by • 0
1
vote
5
replies
4.8k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 9 months ago by ▴ 380 • written 2.9 years ago by ▴ 10
1
vote
7
replies
4.5k
views
Problems Installing biomaRt
biomaRt
updated 6 months ago by 65k • written 2.1 years ago by ▴ 20
2
votes
28
replies
4.5k
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 12 months ago by • 0 • written 6.9 years ago by • 0
0
votes
3
replies
4.3k
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
7
votes
6
replies
4.2k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 7 months ago by 700 • written 21 months ago by ▴ 20
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
4.2k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 6 months ago by • 0 • written 6.4 years ago by ▴ 80
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 9 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 7.9 years ago by ▴ 10
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.9 years ago by ▴ 30
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
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 3.2 years ago by ▴ 10
0
votes
5
replies
3.8k
views
PCA plot for TPM data
PCA
written 6.6 years ago by ▴ 20
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
4
votes
12
replies
3.8k
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
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 50k • written 4.8 years ago by • 0
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 8 weeks ago by • 0 • written 6.4 years ago by ▴ 20
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz Mfuzz
updated 11 days ago by • 0 • written 13.1 years ago by ▴ 720
0
votes
1
reply
3.7k
views
Bioconductor version cannot be validated
Bioconductor Annotation Ann
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
4
replies
3.7k
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 4.5 years ago by • 0
1
vote
11
replies
3.6k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by • 0 • written 10 months ago by • 0
1
vote
4
replies
3.6k
views
ggtree functions suddenly stopped working: "Error in offspring.tbl_tree_item(..."
ggtree
updated 9 months ago by • 0 • written 10 months ago by • 0
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 4 months ago by • 0 • written 4.7 years ago by ▴ 30
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
4
replies
3.5k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 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 8 months ago by • 0 • written 19 months ago by • 0
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 9 weeks ago by • 0 • written 18 months ago by • 0
1
vote
3
replies
3.4k
views
SRAdb: Error downloading sqlite files
sradb
written 6.5 years ago by • 0
2
votes
10
replies
3.3k
views
DESeq2 - Differences between plotCounts and normalized counts
deseq2
updated 7 months ago by 42k • written 5.7 years ago by ▴ 20
2
votes
5
replies
3.2k
views
How to use EnrichGo of Cluster Profiler
EnrichGO clusterProfiler
written 3.3 years ago by • 0
1
vote
2
replies
3.2k
views
Extract genes from ggvenn?
ggvenn
updated 6 weeks ago by ▴ 10 • written 2.0 years ago by • 0
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 8.5 years ago by ▴ 10
2
votes
9
replies
3.2k
views
NCBI Locus ID to gene ID conversion
LocusIDtogeneIDconversion
updated 6 months ago by • 0 • written 20 months ago by ▴ 20
0
votes
5
replies
3.2k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
4
replies
3.2k
views
Problems with FLOWAI
flowAI
written 3.1 years ago by • 0
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
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
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 2 days ago by • 0 • written 5.2 years ago by ▴ 50
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 3 days ago by 42k • written 15 months 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 8 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 10 months ago by • 0 • written 8.1 years ago by ▴ 20
1,738 results • Page 2 of 35
Recent ...
Replies
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…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
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
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
United States, 5 minutes ago
Canada, 5 minutes ago
United States, 8 minutes ago
United States, 17 minutes ago
United States, 35 minutes ago
Traffic: 716 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