0
votes
0
replies
4
views
rtracklayer ignores ranges argument
rtracklayer
31 minutes ago Kyle • 0
0
votes
0
replies
15
views
Changing pathway names in pathway analysis
pathways Pathways
5 hours ago Katharina • 0
1
vote
2
replies
56
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
6 hours ago • updated 5 hours ago stacy.genovese • 0
0
votes
0
replies
14
views
Analyze Amplicon Seq results for variants and mutation sites
virus pcr amplican mutations
6 hours ago Sara • 0
0
votes
0
replies
14
views
DESeq2 parameter infernce
DESeq2parameterinfernce
6 hours ago BioEpi • 0
1
vote
1
reply
45
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 9 hours ago by ★ 2.1k • written 17 hours ago by ▴ 40
0
votes
0
replies
20
views
DESeq2 with 2 continuous factors, LRT, coeficients and slope
DESeq2 LRT continuous coeficients
11 hours ago Laia ▴ 10
0
votes
0
replies
20
views
DESeq2 with sample effect, unequal sample sizes
DESeq2
12 hours ago rf • 0
2
votes
4
replies
66
views
Reproducibility using limma for DE Analysis
limma seed DifferentialRegulation
15 hours ago • updated 13 hours ago TSauer • 0
0
votes
0
replies
14
views
customProDB: error aberrant fasta from SNV
customProDB
15 hours ago finoa.li • 0
0
votes
1
reply
27
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
20 hours ago • updated 19 hours ago liuchangbio • 0
0
votes
0
replies
24
views
Bioconductor tool for curating annotations?
Annotation
21 hours ago Charles Plessy ▴ 170
0
votes
1
reply
47
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
updated 1 day ago by 39k • written 1 day ago by • 0
0
votes
0
replies
35
views
Alternatives to perform peptide identification in Bioconductor version '3.16'?
peptide peptideidentification rTANDEM MSGFplus Alternatives
updated 10 hours ago by 3.4k • written 2 days ago by • 0
0
votes
0
replies
41
views
Distance between columns vs distance between rows and SVD
distance svd
3 days ago Lenny186 • 0
0
votes
3
replies
1.3k
views
Which version of DESeq2 for R 4.1.2 64bit
DESeq2
written 12 months ago by • 0
0
votes
2
replies
75
views
find tandem repeats in DNA
DNA repeats
3 days ago me-nobody • 0
0
votes
0
replies
31
views
Splicing analysis with ASpli package gives an error when I use binGenome function.
S4Vectors Aspli
3 days ago salvocomplicazioni1 • 0
4
votes
1
reply
76
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 3 days ago by ★ 2.1k • written 3 days ago by ▴ 40
0
votes
1
reply
50
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 hours ago by ▴ 50 • written 3 days ago by • 0
0
votes
0
replies
29
views
GOplots::GOChord with heatmaps?
GOChord ggplot2::geom_polygon() GOplot ggplot2
3 days ago adrija.kalvisa • 0
2
votes
10
replies
217
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 1 hour ago by 47k • written 4 days ago by • 0
10
votes
8
replies
214
views
MA plot
MAplot
5 days ago • updated 3 days ago Nathalie ▴ 10
1
vote
3
replies
90
views
transcript name mapping between human and mouse
biomaRt getLDS
updated 3 days ago by 62k • written 4 days ago by • 0
3
votes
2
replies
69
views
I cannot install annotables package in Rstudio (macOS)
DESeq2 PackageTypeData package Annotation
4 days ago • updated 9 hours ago m-bihie ▴ 10
2
votes
3
replies
102
views
How can I draw a barplot of complexheatmap according 'Tumor Type'
heatma heatmaps ComplexHeatmap
updated 4 days ago by ▴ 40 • written 5 days ago by ▴ 10
3
votes
5
replies
139
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 4 days ago by 39k • written 4 days ago by ▴ 10
0
votes
0
replies
34
views
Rsubread align every slow in mac but faster in windows
Rsubread
4 days ago Wei • 0
3
votes
4
replies
110
views
ComplexHeatmap - Default distance and hierarchical clustering methods
ComplexHeatmap Complex
updated 4 days ago by ▴ 40 • written 5 days ago by • 0
0
votes
1
reply
80
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 3 days ago by 39k • written 5 days ago by ▴ 10
0
votes
1
reply
66
views
DESeq2 in R 4.2.2
DESeq2 SummarizedExperiment DelayedArray
updated 4 days ago by ★ 2.1k • written 5 days ago by • 0
0
votes
3
replies
91
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 4 days ago by 62k • written 5 days ago by • 0
0
votes
0
replies
31
views
msa module crash
msa
5 days ago systems • 0
0
votes
0
replies
53
views
News: Seeking members for BioC2023 organizing committee
BioC2023 Bioconductor community
5 days ago • updated 4 days ago Maria Doyle ▴ 10
0
votes
1
reply
71
views
about deltaPSI
SpliceWiz
updated 5 days ago by ▴ 10 • written 5 days ago by • 0
2
votes
2
replies
120
views
Volcano Plot in R
cellxgenedp
updated 5 days ago by 47k • written 6 days ago by ▴ 10
0
votes
1
reply
866
views
limma: decideTests
affy limma affy limma
updated 5 days ago by 47k • written 15.1 years ago by ▴ 270
0
votes
3
replies
124
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
6 days ago • updated 5 days ago martin.grigorov • 0
1
vote
0
replies
121
views
News: Join the Community Advisory Board -- upcoming elections -- deadline January 31st
Bioconductor CAB bioconductoroversight community
6 weeks ago • updated 6 days ago shepherl 3.4k
0
votes
1
reply
56
views
convert local downloaded bigwig files to .bed files
BRgen BRGenomics
updated 6 days ago by ★ 2.1k • written 6 days ago by ▴ 20
0
votes
1
reply
68
views
NAs in some genes in topTable output
limma topTable
updated 6 days ago by 47k • written 6 days ago by ▴ 10
0
votes
1
reply
56
views
limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 6 days ago by 47k • written 6 days ago by • 0
0
votes
1
reply
88
views
Libraries loading error
DESeq2 clusterProfiler enrichplot
updated 6 days ago by 39k • written 11 days ago by • 0
0
votes
1
reply
75
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 6 days ago by 39k • written 7 days ago by • 0
1
vote
4
replies
133
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 17 hours ago by ▴ 30 • written 7 days ago by • 0
0
votes
1
reply
61
views
Subset count data in DGEList using edgeR/DESeq2
edgeR DMR
updated 6 days ago by 39k • written 7 days ago by • 0
0
votes
2
replies
75
views
scanBam
Rsamtools Rsam
updated 6 days ago by 25k • written 8 days ago by • 0
2
votes
3
replies
104
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 7 days ago by 62k • written 7 days ago by • 0
0
votes
0
replies
23
views
INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
7 days ago MK • 0
0
votes
2
replies
89
views
Diffbind (or maybe DESeq2) Fold clarification
DiffBind
updated 7 days ago by ★ 4.6k • written 11 days ago by • 0
43,715 results • Page 1 of 875
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
`PoolStatus` just indicates whether a sample is a pool or not, i.e., the first option.
Comment: How to map geneIds to ENTREZIDs by stacy.genovese • 0
James - I wish I knew where you lived so I could buy you a beer! Thank you so much for your help. I'm going to work now on converting th…
Answer: How to map geneIds to ENTREZIDs by James W. MacDonald 62k
You are close. But note that the geneIds in your `GRanges` object are NCBI Gene IDs, which used to be called Entrez Gene IDs, and which are…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Just so I don't make a mistake, do I just tell voomLmFit if a sample is a pool or a replicate independent of each group, or do I have to sp…
Comment: I cannot install annotables package in Rstudio (macOS) by m-bihie ▴ 10
thanks, this worked!
Votes
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: How to map geneIds to ENTREZIDs
Comment: ComplexHeatmap - Default distance and hierarchical clustering methods
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Awards • All
Scholar to James W. MacDonald 62k
Commentator to vs2001 ▴ 30
Scholar to Mike Smith ★ 5.9k
Popular Question to shepherl 3.4k
Scholar to Gordon Smyth 47k
Locations • All
WEHI, Melbourne, Australia, 14 minutes ago
Australia, 26 minutes ago
Australia/Melbourne/Olivia Newton-John Cancer Research Institute, 49 minutes ago
Melbourne, Australia, 49 minutes ago
United States, 53 minutes ago
Traffic: 325 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