0
votes
0
replies
16
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
8 hours ago ja.garcia • 0
1
vote
2
replies
187
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 8 weeks ago by • 0
0
votes
2
replies
46k
views
SingleR Label.Ont
SingleR
written 16 months ago by • 0
0
votes
0
replies
20
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
11 hours ago brown.annaleigh • 0
0
votes
0
replies
16
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
16 hours ago xiaofeiwang18266 ▴ 50
0
votes
0
replies
22
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
21 hours ago sarah.williams • 0
2
votes
5
replies
353
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 1 day ago by 67k • written 1 day ago by ▴ 10
0
votes
1
reply
75
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 1 day ago by 67k • written 3 days ago by • 0
0
votes
2
replies
105
views
Error using useMart or useEnsembl
biomaRt
updated 1 day ago by 67k • written 1 day ago by • 0
2
votes
1
reply
94
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 1 day ago by 67k • written 1 day ago by ▴ 50
0
votes
11
replies
376
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 4 hours ago by 43k • written 2 days ago by • 0
0
votes
2
replies
194
views
DESeq2 Heatmap
heatmaps
updated 2 days ago by ★ 1.4k • written 3 days ago by • 0
0
votes
4
replies
189
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 2 days ago by 67k • written 2 days ago by • 0
0
votes
1
reply
79
views
Unknown gene transcripts after annotatr
annotatr
updated 2 days ago by 67k • written 2 days ago by • 0
0
votes
1
reply
71
views
Improve performance of qusage aggregateGeneSet
qusage
updated 3 days ago by 67k • written 3 days ago by • 0
0
votes
0
replies
53
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
4 days ago • updated 3 days ago nurkenber • 0
0
votes
0
replies
41
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
4 days ago GJ • 0
0
votes
1
reply
68
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 4 days ago by 67k • written 4 days ago by ▴ 20
0
votes
0
replies
38
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
5 days ago info ▴ 10
0
votes
1
reply
122
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 4 days ago by 4.1k • written 6 days ago by • 0
0
votes
2
replies
342
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 7 days ago by ▴ 840
0
votes
2
replies
209
views
iam not able to do retrive data using GEOquery R package
HELP
updated 7 days ago by 67k • written 7 days ago by • 0
2
votes
5
replies
275
views
Differential variability modelling with vst() expression
limma DESeq2
written 8 days ago by • 0
0
votes
2
replies
116
views
Installation error for Rsamtools.
Rsamtools
updated 7 days ago by ★ 4.6k • written 8 days ago by • 0
2
votes
8
replies
488
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 7 days ago by 67k • written 8 days ago by • 0
0
votes
2
replies
334
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
8 days ago • updated 6 days ago sindhuri • 0
0
votes
0
replies
47
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
9 days ago Maggie • 0
2
votes
9
replies
691
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
updated 2 days ago by 43k • written 9 days ago by ▴ 10
0
votes
5
replies
215
views
Diffbind interpretation of data - fold change
DiffBind
10 days ago Vera • 0
1
vote
1
reply
265
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 10 days ago by 43k • written 10 days ago by • 0
0
votes
1
reply
75
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 10 days ago by 67k • written 10 days ago by • 0
1
vote
2
replies
293
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV genefu
10 days ago Levi Waldron ★ 1.1k
0
votes
0
replies
44
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
11 days ago vpochic • 0
0
votes
4
replies
211
views
Newbie Question - adding metadata to an analysis
Biobase
11 days ago • updated 9 days ago Bryan H • 0
0
votes
1
reply
146
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 days ago by ★ 1.4k • written 11 days ago by • 0
0
votes
2
replies
237
views
MissMethyl failed to use gometh function for EPICv2
missMethyl EPICv2manifest
updated 11 days ago by 67k • written 11 days ago by • 0
0
votes
1
reply
101
views
Correlation between gene clusters
genomes RNASeqData
written 11 days ago by • 0
0
votes
2
replies
195
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
13 days ago • updated 11 days ago gingergeiger22 • 0
0
votes
0
replies
64
views
Error ("could not find function "EM_estimate"") when running ENmix mpreprocess() on Microsoft Azure
Preprocessing ENmix
13 days ago balf0020 • 0
0
votes
1
reply
330
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 14 days ago by 43k • written 24 days ago by • 0
2
votes
1
reply
331
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 14 days ago by 43k • written 21 days ago by • 0
0
votes
1
reply
1.3k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 15 days ago by • 0 • written 3.1 years ago by ▴ 50
6
votes
5
replies
518
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 10 days ago by 67k • written 16 days ago by • 0
1
vote
8
replies
787
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
17 days ago • updated 10 days ago Andre • 0
0
votes
2
replies
244
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
19 days ago • updated 18 days ago Kucsera • 0
0
votes
1
reply
169
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 22 days ago by • 0 • written 24 days ago by • 0
0
votes
3
replies
1.2k
views
News: EuroBioC2023 abstract submission closing soon!
presentation EuroBioc2023 Conference community Bioconductor
written 21 months ago by ▴ 90
0
votes
5
replies
1.2k
views
News: EuroBioC2024 abstract submission is open!
Conference Bioconductor EuroBioC2024
updated 21 days ago by • 0 • written 11 months ago by ▴ 90
0
votes
2
replies
442
views
Cross-validation with multiple control subgroups in limma
limma multtest
28 days ago • updated 26 days ago Ali Barry ▴ 40
1
vote
1
reply
357
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 28 days ago by 43k • written 5 weeks ago by • 0
46,294 results • Page 1 of 926
Recent ...
Replies
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
Awards • All
Popular Question to Bob ▴ 10
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Scholar to James W. MacDonald 67k
Popular Question to Assa Yeroslaviz ★ 1.5k
Locations • All
Australia, 5 minutes ago
United States, 5 minutes ago
New Zealand, 1 hour ago
Canada, 1 hour ago
United States, 2 hours ago
Traffic: 578 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