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207
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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 3 months ago by 68k • written 3 months ago by • 0
6
votes
10
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2.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 4 months ago by ★ 4.8k • written 5 months ago by ▴ 10
0
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0
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285
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
6 months ago Anke • 0
1
vote
1
reply
620
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 7 months ago by 68k • written 7 months ago by • 0
2
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3
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740
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 9 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 12 months ago by • 0 • written 6.2 years ago by • 0
0
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0
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405
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
14 months ago danalvoronov ▴ 10
0
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4
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885
views
limma with interaction term
R biostatistics limma Epigenetics
14 months ago Jitendra ▴ 10
0
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3
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2.2k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.2 years ago by • 0
1
vote
5
replies
2.6k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.2 years ago by ▴ 10
0
votes
8
replies
3.2k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 10 days ago by • 0 • written 16 months ago by • 0
0
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0
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545
views
multipollutant models
statistics Regression r limma
17 months ago Jitendra ▴ 10
3
votes
4
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1.1k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
17 months ago pl23 • 0
1
vote
3
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2.3k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 17 months ago by ▴ 750 • written 4.0 years ago by • 0
0
votes
10
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1.5k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
17 months ago • updated 14 months ago ScafioRuo • 0
12
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10
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15k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 13 months ago by • 0 • written 18 months ago by ▴ 20
0
votes
2
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1.0k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
20 months ago • updated 19 months ago yr542 • 0
1
vote
2
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1.2k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
21 months ago Miguel • 0
2
votes
5
replies
1.9k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
21 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
842
views
Gene enrichment analysis
analysis R GOfuncR
updated 22 months ago by ▴ 760 • written 22 months ago by • 0
0
votes
2
replies
1.7k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 23 months ago by • 0 • written 4.2 years ago by • 0
0
votes
1
reply
969
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 24 months ago by 52k • written 24 months ago by • 0
0
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1
reply
764
views
DEseq2 Single cell data paired design
R
updated 2.0 years ago by ▴ 30 • written 2.0 years ago by • 0
0
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4
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1.5k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
1
vote
3
replies
1.4k
views
tximport error
tximport r
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
1
vote
2
replies
1.5k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.0 years ago Abdul ▴ 20
0
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0
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768
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.0 years ago aymanreffai • 0
1
vote
1
reply
2.8k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Unable to install BiocManager
Biocmanager R
updated 2.0 years ago by ▴ 50 • written 2.0 years ago by • 0
1
vote
1
reply
1.9k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
0
votes
13
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11k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.1 years ago Laia ▴ 10
1
vote
3
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7.7k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 2.1 years ago by ★ 4.1k • written 2.2 years ago by ▴ 10
0
votes
1
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1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
0
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0
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747
views
rDGIdb package: score of the results
rDGIdb r
2.1 years ago HELEN • 0
2
votes
1
reply
766
views
add column with name in R
name R column
updated 2.1 years ago by ▴ 70 • written 2.1 years ago by • 0
0
votes
4
replies
1.6k
views
how to extract list in quantile in R
R quantile list
2.1 years ago sat • 0
0
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0
replies
1.1k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
2.1 years ago Manav • 0
0
votes
0
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871
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
2.2 years ago Jitendra ▴ 10
3
votes
2
replies
1.4k
views
how to extract and match information of two filein R
R column match
2.2 years ago sat • 0
0
votes
0
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797
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.2 years ago info ▴ 10
0
votes
17
replies
2.5k
views
How to check linear model
modalmatrix limma R linear
2.2 years ago Jitendra ▴ 10
0
votes
1
reply
1.1k
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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3
replies
1.8k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 2.2 years ago by ▴ 760 • written 2.2 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
2.2 years ago abhisek001 • 0
0
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4
replies
1.5k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.2 years ago Dr. • 0
0
votes
1
reply
1.6k
views
Extract Intersection Values from Venn
R Venn
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
votes
6
replies
2.5k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.2 years ago yr542 • 0
0
votes
0
replies
786
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.2 years ago Luomeng • 0
2
votes
9
replies
1.8k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
2
replies
4.2k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.2 years ago by 52k • written 2.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Comment: Intepretation of results by Tom • 0
[Locksmith Wombwell][1] I have been interested in using AUCell as a way to determine significantly enriched pathways in my single cell spat…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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