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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 10 months ago by 68k • written 10 months ago by • 0
6
votes
10
replies
3.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
0
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0
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446
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
14 months ago Anke • 0
1
vote
1
reply
808
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 15 months ago by 68k • written 15 months ago by • 0
2
votes
3
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971
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 16 months ago by • 0
3
votes
3
replies
16k
views
How to fix 'long vectors not supported yet' error in R
r
updated 20 months ago by • 0 • written 6.8 years ago by • 0
0
votes
0
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629
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
21 months ago danalvoronov ▴ 10
0
votes
4
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1.1k
views
limma with interaction term
R biostatistics limma Epigenetics
22 months ago • updated 21 months ago Jitendra ▴ 10
0
votes
3
replies
2.4k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.8 years ago by • 0
1
vote
5
replies
2.8k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.8 years ago by ▴ 10
0
votes
10
replies
3.8k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 2.0 years ago by • 0
0
votes
0
replies
707
views
multipollutant models
statistics Regression r limma
2.0 years ago Jitendra ▴ 10
3
votes
4
replies
1.4k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.0 years ago pl23 • 0
1
vote
3
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2.6k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 2.1 years ago by ▴ 750 • written 4.6 years ago by • 0
0
votes
10
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1.9k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
2.1 years ago • updated 21 months ago ScafioRuo • 0
12
votes
10
replies
16k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 20 months ago by • 0 • written 2.1 years ago by ▴ 20
0
votes
2
replies
1.3k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.3 years ago • updated 2.2 years ago yr542 • 0
1
vote
2
replies
1.4k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
2.4 years ago Miguel • 0
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.4 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.1k
views
Gene enrichment analysis
analysis R GOfuncR
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by • 0
0
votes
2
replies
1.9k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 2.5 years ago by • 0 • written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
1
reply
890
views
DEseq2 Single cell data paired design
R
updated 2.6 years ago by ▴ 30 • written 2.6 years ago by • 0
0
votes
4
replies
1.8k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
1
vote
3
replies
1.6k
views
tximport error
tximport r
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
vote
2
replies
1.8k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.6 years ago Abdul ▴ 20
0
votes
0
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931
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.6 years ago aymanreffai • 0
1
vote
1
reply
3.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
0
votes
4
replies
1.7k
views
Unable to install BiocManager
Biocmanager R
updated 2.6 years ago by ▴ 50 • written 2.7 years ago by • 0
1
vote
1
reply
2.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
13
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13k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.7 years ago Laia ▴ 10
1
vote
3
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8.6k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 2.7 years ago by ★ 4.1k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.6k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
0
votes
0
replies
872
views
rDGIdb package: score of the results
rDGIdb r
2.7 years ago HELEN • 0
2
votes
1
reply
890
views
add column with name in R
name R column
updated 2.7 years ago by ▴ 70 • written 2.7 years ago by • 0
0
votes
4
replies
1.9k
views
how to extract list in quantile in R
R quantile list
2.7 years ago sat • 0
0
votes
0
replies
1.3k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
2.8 years ago Manav • 0
0
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0
replies
1.1k
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
2.8 years ago Jitendra ▴ 10
3
votes
2
replies
1.6k
views
how to extract and match information of two filein R
R column match
2.8 years ago sat • 0
0
votes
0
replies
1.0k
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.8 years ago info ▴ 10
0
votes
17
replies
3.0k
views
How to check linear model
modalmatrix limma R linear
2.8 years ago Jitendra ▴ 10
0
votes
1
reply
1.3k
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
3
replies
2.1k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
2.8 years ago abhisek001 • 0
0
votes
4
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1.7k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.8 years ago Dr. • 0
0
votes
1
reply
1.8k
views
Extract Intersection Values from Venn
R Venn
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
2
votes
6
replies
2.8k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.8 years ago yr542 • 0
0
votes
0
replies
922
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.8 years ago Luomeng • 0
2
votes
9
replies
2.2k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
1
vote
2
replies
4.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.8 years ago by 53k • written 2.9 years ago by • 0
1,163 results • Page 1 of 24
Recent ...
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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