4
votes
3
replies
654
views
plyranges: find exact GRanges match keeping metadata columns
plyranges
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
426
views
News: Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
11 months ago info ▴ 10
0
votes
1
reply
453
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP csaw
updated 11 months ago by ★ 29k • written 11 months ago by • 0
0
votes
0
replies
303
views
Batch Correction while implementing QSEA package
qsea MEDIPS MEDIPSData DNAMethylation
11 months ago User3088 • 0
0
votes
0
replies
315
views
News: Announcing the GBCC2025 Logo Design Winner!
Community Conference GBCC2025 Bioconductor
11 months ago Maria Doyle ▴ 110
0
votes
1
reply
480
views
building samplesheet and plot profile
DiffBind
11 months ago yf • 0
0
votes
0
replies
217
views
DBT JRF & PhD Scholar
BiologicalQuestion OmicsMLRepoR
11 months ago Manisha • 0
0
votes
1
reply
445
views
I am having issues with bowtie2_build
genomes bowtiew Index
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
698
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
382
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
11 months ago cftattersfield • 0
1
vote
0
replies
647
views
News: Bioconductor Course, Kenya 2025: Applications Open!
Events Community Training Africa Bioconductor
11 months ago Maria Doyle ▴ 110
0
votes
2
replies
998
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
11 months ago • updated 10 months ago ingrid.h • 0
2
votes
2
replies
739
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
9
votes
3
replies
2.6k
views
Job: Postdoc/RA position: Software Engineer For R and High-Performance Computing
JobPosting CuratedAtlasQueryR tidySpatialExperiment tidyomics tidySingleCellExperiment
written 18 months ago by ▴ 40
0
votes
4
replies
1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
11 months ago Quang NN ▴ 10
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 11 months ago by • 0 • written 11 months ago by • 0
4
votes
9
replies
3.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 11 months ago by ★ 3.4k • written 12 months ago by ▴ 20
0
votes
1
reply
651
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
2
replies
608
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
11 months ago Vinesh • 0
0
votes
1
reply
373
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
1
reply
402
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
2
replies
1.5k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
11 months ago Blandine • 0
0
votes
5
replies
787
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 11 months ago by • 0
0
votes
1
reply
484
views
affymetrix
genomes Annotation
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
2.2k
views
Problems with GSEA
GSEABase
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
1
reply
550
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
11 months ago ja.garcia • 0
0
votes
4
replies
1.1k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
11 months ago Quang NN ▴ 10
2
votes
4
replies
1.0k
views
EdgeR Biological CVs
edgeR
written 11 months ago by • 0
0
votes
1
reply
541
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
272
views
Problem with PCAtool as dependencie
COTAN PCAtools
11 months ago Silvia • 0
1
vote
2
replies
487
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 13 months ago by • 0
0
votes
0
replies
330
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
11 months ago xiaofeiwang18266 ▴ 60
3
votes
5
replies
2.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 11 months ago by 68k • written 11 months ago by ▴ 10
0
votes
1
reply
428
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 11 months ago by 68k • written 12 months ago by • 0
0
votes
2
replies
1.8k
views
Error using useMart or useEnsembl
biomaRt
updated 11 months ago by 68k • written 11 months ago by • 0
2
votes
1
reply
802
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 11 months ago by 68k • written 11 months ago by ▴ 60
0
votes
11
replies
1.5k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
1.0k
views
DESeq2 Heatmap
heatmaps
updated 11 months ago by ★ 1.4k • written 12 months ago by • 0
0
votes
4
replies
2.1k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
346
views
Unknown gene transcripts after annotatr
annotatr
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
357
views
Improve performance of qusage aggregateGeneSet
qusage
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
0
replies
337
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
12 months ago nurkenber • 0
0
votes
0
replies
403
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
12 months ago GJ • 0
0
votes
1
reply
432
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 12 months ago by 68k • written 12 months ago by ▴ 20
0
votes
0
replies
558
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
12 months ago info ▴ 10
0
votes
2
replies
703
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 months ago by ▴ 840
0
votes
2
replies
918
views
iam not able to do retrive data using GEOquery R package
HELP
updated 12 months ago by 68k • written 12 months ago by • 0
2
votes
5
replies
910
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 0
0
votes
2
replies
542
views
Installation error for Rsamtools.
Rsamtools
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
3
votes
9
replies
2.2k
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 11 months ago by • 0 • written 12 months ago by • 0
46,711 results • Page 10 of 935
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Teacher to Michael Love 43k
Popular Question to lianov • 0
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
United States, 2 hours ago
United States, 3 hours ago
Barcelona, Spain, 3 hours ago
United States, 4 hours ago
Traffic: 1445 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