3
votes
8
replies
558
views
Downloading package mixOmics
mixOmics
12 weeks ago noortje_bloem94 • 0
3
votes
4
replies
259
views
Help with error using camera() in limma
CAMERA limma
16 days ago Chris ▴ 10
3
votes
4
replies
502
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
3
votes
5
replies
284
views
Help with running egsea()
EGSEA
10 days ago • updated 9 days ago Chris ▴ 10
3
votes
5
replies
906
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
3
votes
2
replies
464
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
6
replies
716
views
Methylation data analysis
MethylationArrayData methylationArrayAnalysis
6 months ago aldea85 • 0
3
votes
5
replies
1.7k
views
Error: 'IdClusters'
DECIPHER
updated 11 months ago by ▴ 10 • written 15 months ago by • 0
3
votes
2
replies
581
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 6 weeks ago by • 0 • written 5.2 years ago by • 0
3
votes
1
reply
440
views
NPARC package y-variable
NPARC NPA
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
3
votes
6
replies
304
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
3
votes
6
replies
858
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
5
replies
1.2k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor Install library biocmanager
updated 10 months ago by 6.7k • written 10 months ago by ▴ 20
3
votes
5
replies
664
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
votes
3
replies
9.5k
views
How to find rsID with biomaRt in R
biomaRt
updated 3 months ago by 65k • written 3.2 years ago by ▴ 10
3
votes
7
replies
1.9k
views
Installing densvis on a Singularity container
densvis docker
updated 11 months ago by ▴ 160 • written 12 months ago by 65k
3
votes
5
replies
891
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
8 months ago Ethan Nguyen • 0
3
votes
8
replies
930
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
3
votes
16
replies
2.2k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.9k • written 2.9 years ago by ▴ 10
3
votes
6
replies
23k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 4 months ago by • 0 • written 5.7 years ago by • 0
3
votes
18
replies
3.0k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 29 days ago shepherl 3.9k
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.1k • written 6.4 years ago by • 0
3
votes
2
replies
687
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
6
replies
2.2k
views
Result from GSEA for non-model organism not as expected
clusterProfiler
updated 5 months ago by 65k • written 19 months ago by ▴ 10
3
votes
5
replies
923
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 18 months ago by • 0
3
votes
4
replies
557
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
3
votes
2
replies
493
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
3
votes
6
replies
1.0k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
10 months ago abhisek001 • 0
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
3
votes
5
replies
1.4k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 29 days ago jacques.imbert • 0
3
votes
6
replies
585
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
12 weeks ago boczniak767 ▴ 720
3
votes
3
replies
1.5k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 3 months ago by • 0 • written 5.0 years ago by ▴ 10
3
votes
1
reply
326
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months 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
3
votes
3
replies
568
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
3
votes
1
reply
144
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by 42k • written 10 days ago by • 0
3
votes
4
replies
265
views
Store output of matchPWM()
biostrings Biostrings
15 days ago • updated 3 days ago mat149 ▴ 70
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 9 days ago by 50k • written 5.6 years ago by ▴ 10
3
votes
2
replies
298
views
Question about DMRcate
DMRcate dmrcate
3 months ago chuanjiao6 • 0
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 6 months ago by • 0 • written 4.8 years ago by ▴ 50
3
votes
1
reply
765
views
News: [Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv spatialLIBD News
written 4.2 years ago by ★ 1.0k
3
votes
1
reply
1.5k
views
Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job Job machine learning deep learning computational biology
written 6.3 years ago by ▴ 180
3
votes
6
replies
2.8k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 12 weeks ago by • 0 • written 5.3 years ago by ▴ 50
3
votes
3
replies
589
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 8 months ago by • 0
1,739 results • Page 4 of 35
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
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 shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Locations • All
Spain, 8 minutes ago
Greece, 10 minutes ago
India, 34 minutes ago
Denmark, 37 minutes ago
United States, 58 minutes ago
Traffic: 717 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