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102
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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 11 days ago by 67k • written 13 days ago by • 0
6
votes
10
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2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 7 weeks ago by ★ 4.6k • written 8 weeks ago by ▴ 10
0
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0
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209
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[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
3 months ago Anke • 0
1
vote
1
reply
456
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 4 months ago by 67k • written 4 months ago by • 0
2
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3
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624
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 6 months ago by • 0
3
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3
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15k
views
How to fix 'long vectors not supported yet' error in R
r
updated 9 months ago by • 0 • written 6.0 years ago by • 0
0
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0
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351
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
11 months ago danalvoronov ▴ 10
0
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4
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760
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limma with interaction term
R biostatistics limma Epigenetics
11 months ago Jitendra ▴ 10
0
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3
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2.0k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.9 years ago by • 0
1
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5
replies
2.5k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.0 years ago by ▴ 10
0
votes
7
replies
2.1k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 13 months ago by • 0
0
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0
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495
views
multipollutant models
statistics Regression r limma
14 months ago Jitendra ▴ 10
3
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4
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1.0k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
14 months ago pl23 • 0
1
vote
3
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2.1k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 14 months ago by ▴ 750 • written 3.7 years ago by • 0
0
votes
10
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1.4k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
14 months ago • updated 11 months ago ScafioRuo • 0
12
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10
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13k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 10 months ago by • 0 • written 15 months ago by ▴ 20
0
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2
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905
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
17 months ago • updated 16 months ago yr542 • 0
1
vote
2
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1.0k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
18 months ago Miguel • 0
2
votes
5
replies
1.7k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
18 months ago mohammedtoufiq91 ▴ 10
0
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1
reply
786
views
Gene enrichment analysis
analysis R GOfuncR
updated 19 months ago by ▴ 760 • written 19 months ago by • 0
0
votes
2
replies
1.6k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 20 months ago by • 0 • written 3.9 years ago by • 0
0
votes
1
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899
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 21 months ago by 52k • written 21 months ago by • 0
0
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1
reply
720
views
DEseq2 Single cell data paired design
R
updated 21 months ago by ▴ 30 • written 21 months ago by • 0
0
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4
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1.4k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 21 months ago by ★ 1.4k • written 21 months ago by • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 21 months ago by 43k • written 21 months ago by • 0
1
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2
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1.3k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
21 months ago Abdul ▴ 20
0
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0
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713
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
21 months ago aymanreffai • 0
1
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1
reply
2.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 21 months ago by ★ 4.1k • written 21 months ago by ▴ 10
0
votes
4
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1.3k
views
Unable to install BiocManager
Biocmanager R
updated 21 months ago by ▴ 50 • written 21 months ago by • 0
1
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1
reply
1.8k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 22 months ago by • 0 • written 22 months ago by • 0
0
votes
13
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8.8k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
22 months ago Laia ▴ 10
1
vote
3
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6.6k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 22 months ago by ★ 4.1k • written 23 months ago by ▴ 10
0
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1
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1.1k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 22 months ago by ▴ 750 • written 22 months ago by ▴ 10
0
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0
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703
views
rDGIdb package: score of the results
rDGIdb r
22 months ago HELEN • 0
2
votes
1
reply
709
views
add column with name in R
name R column
updated 22 months ago by ▴ 70 • written 22 months ago by • 0
0
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4
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1.4k
views
how to extract list in quantile in R
R quantile list
23 months ago sat • 0
0
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0
replies
942
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
23 months ago Manav • 0
0
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0
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778
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
23 months ago Jitendra ▴ 10
3
votes
2
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1.2k
views
how to extract and match information of two filein R
R column match
23 months ago sat • 0
0
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0
replies
750
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
23 months ago info ▴ 10
0
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17
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2.3k
views
How to check linear model
modalmatrix limma R linear
23 months ago Jitendra ▴ 10
0
votes
1
reply
1.0k
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 23 months ago by 67k • written 23 months ago by • 0
0
votes
3
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1.6k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 23 months ago by ▴ 760 • written 23 months ago by ▴ 10
1
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2
replies
1.2k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
23 months ago abhisek001 • 0
0
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4
replies
1.3k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
23 months ago Dr. • 0
0
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1
reply
1.4k
views
Extract Intersection Values from Venn
R Venn
updated 23 months ago by 67k • written 23 months ago by • 0
2
votes
6
replies
2.3k
views
DMRcate
DMRcate R DMRcatedata Markdown
23 months ago yr542 • 0
0
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0
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731
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
24 months ago Luomeng • 0
2
votes
9
replies
1.6k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 24 months ago by 67k • written 24 months ago by • 0
1
vote
2
replies
3.5k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 24 months ago by 52k • written 2.0 years ago by • 0
50 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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