0
votes
1
reply
257
views
Improve performance of qusage aggregateGeneSet
qusage
updated 8 months ago by 68k • written 8 months ago by • 0
0
votes
0
replies
276
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
8 months ago nurkenber • 0
0
votes
0
replies
328
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
8 months ago GJ • 0
0
votes
1
reply
274
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 8 months ago by 68k • written 8 months ago by ▴ 20
0
votes
0
replies
404
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
8 months ago info ▴ 10
0
votes
2
replies
609
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 8 months ago by ▴ 840
0
votes
2
replies
756
views
iam not able to do retrive data using GEOquery R package
HELP
updated 8 months ago by 68k • written 8 months ago by • 0
2
votes
5
replies
716
views
Differential variability modelling with vst() expression
limma DESeq2
written 8 months ago by • 0
0
votes
2
replies
432
views
Installation error for Rsamtools.
Rsamtools
updated 8 months ago by ★ 4.9k • written 8 months ago by • 0
3
votes
9
replies
1.8k
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 months ago by • 0 • written 8 months ago by • 0
0
votes
3
replies
824
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 months ago by • 0
0
votes
2
replies
825
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 6 months ago by • 0 • written 8 months ago by • 0
2
votes
9
replies
1.5k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
8 months ago • updated 7 months ago Quang NN ▴ 10
0
votes
5
replies
691
views
Diffbind interpretation of data - fold change
DiffBind
8 months ago Vera • 0
1
vote
1
reply
807
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
470
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 8 months ago by 68k • written 8 months ago by • 0
1
vote
2
replies
3.0k
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV genefu
8 months ago Levi Waldron ★ 1.1k
0
votes
0
replies
272
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
8 months ago vpochic • 0
0
votes
4
replies
501
views
Newbie Question - adding metadata to an analysis
Biobase
8 months ago Bryan H • 0
0
votes
1
reply
321
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
2
replies
518
views
MissMethyl failed to use gometh function for EPICv2
missMethyl EPICv2manifest
updated 8 months ago by 68k • written 8 months ago by • 0
0
votes
1
reply
398
views
Correlation between gene clusters
genomes RNASeqData
written 8 months ago by • 0
0
votes
2
replies
594
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
8 months ago gingergeiger22 • 0
0
votes
1
reply
556
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
2
votes
1
reply
579
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
1
reply
1.6k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 8 months ago by • 0 • written 3.8 years ago by ▴ 60
6
votes
5
replies
977
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 8 months ago by 68k • written 8 months ago by • 0
1
vote
8
replies
1.5k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
8 months ago Andre • 0
0
votes
2
replies
670
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
8 months ago Kucsera • 0
0
votes
1
reply
516
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 8 months ago by • 0 • written 8 months ago by • 0
0
votes
4
replies
2.1k
views
News: EuroBioC2023 abstract submission closing soon!
presentation EuroBioc2023 Conference community Bioconductor
written 2.4 years ago by ▴ 100
0
votes
2
replies
725
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Cross-validation with multiple control subgroups in limma
limma multtest
8 months ago Ali Barry ▴ 40
1
vote
1
reply
525
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 8 months ago by 43k • written 9 months ago by • 0
0
votes
1
reply
491
views
Job: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
updated 8 months ago by • 0 • written 9 months ago by ★ 2.0k
0
votes
1
reply
600
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 8 months ago by • 0 • written 9 months ago by • 0
1
vote
9
replies
1.4k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 months ago by ▴ 30
0
votes
2
replies
981
views
Error in get_anno_data(ontology) : ontology not supported yet...
EnrichDO
9 months ago GODseeker • 0
4
votes
2
replies
915
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 months ago by ★ 4.9k • written 9 months ago by ▴ 10
0
votes
2
replies
547
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Build error on kunpeng2 Linux aarch64
Bioconductor
updated 8 months ago by • 0 • written 9 months ago by • 0
0
votes
3
replies
1.6k
views
Limma - using both array and spot weights in lmFit
Genetics Genetics
written 18.4 years ago by ▴ 170
0
votes
2
replies
623
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Margins for gene_set_enrichment_plot
spatialLIBD
updated 9 months ago by ★ 1.1k • written 9 months ago by • 0
0
votes
1
reply
274
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 9 months ago by • 0
0
votes
2
replies
784
views
Need new version : tx2gene.gencode.v47.csv
tximportData
9 months ago • updated 3 months ago Gaurav • 0
1
vote
5
replies
907
views
Deseq2 Design
RNASeq DESeq2
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
5
replies
1.0k
views
p value is 0, padj is 0
DESeq2
9 months ago Wirayatida • 0
0
votes
2
replies
1.6k
views
Cannot install GO.db and org.Hs.eg.db
Install
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
5
replies
873
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 9 months ago by • 0
1
vote
2
replies
1.1k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 months ago georgii.vdovin • 0
0
votes
1
reply
793
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 9 months ago by 53k • written 18 months ago by • 0
0
votes
0
replies
10
views
Spam: Best Hotels In Maui
prebs
9 months ago 2zrcj3448p 0
46,625 results • Page 9 of 933
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
Normalization or filtering are never done for subsets of samples in any limma or edgeR analysis. These things must always be done globally.
Answer: DESeq2 interactions by swbarnes2 ★ 1.4k
The simpler way to do the first four comparisons is to make a new column in colData that is temp_pollution, and specify that column alone a…
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
You are. The reason I pointed you to `forgeBSgenomeDataPkgFromTwobitFile` is because it's much simpler, doesn't require a seed file, and is…
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by mat149 ▴ 80
I've tried the following, but I must be missing something: setwd("C:\\Users\\....\\wd\\dump\\seqs_srcdir") e122<-readDNA…
Comment: readBam vs read_bam_insert_metrics by rtrivedi1 ▴ 10
Thanks for the answer.
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Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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