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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 7 months ago by 68k • written 7 months ago by • 0
6
votes
10
replies
3.2k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 8 months ago by ★ 4.9k • written 8 months ago by ▴ 10
0
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0
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363
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[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
10 months ago Anke • 0
1
vote
1
reply
751
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 11 months ago by 68k • written 11 months ago by • 0
2
votes
3
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848
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 13 months ago by • 0
3
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3
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16k
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How to fix 'long vectors not supported yet' error in R
r
updated 16 months ago by • 0 • written 6.5 years ago by • 0
0
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0
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472
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
17 months ago danalvoronov ▴ 10
0
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4
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1.0k
views
limma with interaction term
R biostatistics limma Epigenetics
18 months ago Jitendra ▴ 10
0
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3
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2.3k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.5 years ago by • 0
1
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5
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2.7k
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pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.5 years ago by ▴ 10
0
votes
9
replies
3.5k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 22 days ago by • 0 • written 20 months ago by • 0
0
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0
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621
views
multipollutant models
statistics Regression r limma
21 months ago Jitendra ▴ 10
3
votes
4
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1.3k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
21 months ago pl23 • 0
1
vote
3
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2.5k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 21 months ago by ▴ 750 • written 4.3 years ago by • 0
0
votes
10
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1.7k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
21 months ago • updated 17 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 17 months ago by • 0 • written 22 months ago by ▴ 20
0
votes
2
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1.1k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.0 years ago • updated 23 months ago yr542 • 0
1
vote
2
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1.3k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
2.1 years ago Miguel • 0
2
votes
5
replies
2.0k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.1 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
931
views
Gene enrichment analysis
analysis R GOfuncR
updated 2.2 years ago by ▴ 760 • written 2.2 years ago by • 0
0
votes
2
replies
1.8k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 2.2 years ago by • 0 • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
votes
1
reply
830
views
DEseq2 Single cell data paired design
R
updated 2.3 years ago by ▴ 30 • written 2.3 years ago by • 0
0
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4
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1.6k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
1
vote
3
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1.5k
views
tximport error
tximport r
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
vote
2
replies
1.6k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.4 years ago Abdul ▴ 20
0
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0
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859
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
2.4 years ago aymanreffai • 0
1
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1
reply
3.1k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 10
0
votes
4
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1.6k
views
Unable to install BiocManager
Biocmanager R
updated 2.4 years ago by ▴ 50 • written 2.4 years ago by • 0
1
vote
1
reply
2.1k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
0
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13
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13k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.4 years ago Laia ▴ 10
1
vote
3
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8.2k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 2.4 years ago by ★ 4.1k • written 2.5 years ago by ▴ 10
0
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1
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1.4k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.4 years ago by ▴ 760 • written 2.4 years ago by ▴ 10
0
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0
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809
views
rDGIdb package: score of the results
rDGIdb r
2.4 years ago HELEN • 0
2
votes
1
reply
828
views
add column with name in R
name R column
updated 2.4 years ago by ▴ 70 • written 2.4 years ago by • 0
0
votes
4
replies
1.7k
views
how to extract list in quantile in R
R quantile list
2.5 years ago sat • 0
0
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0
replies
1.2k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
2.5 years ago Manav • 0
0
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0
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983
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
2.5 years ago Jitendra ▴ 10
3
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2
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1.5k
views
how to extract and match information of two filein R
R column match
2.5 years ago sat • 0
0
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0
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893
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.5 years ago info ▴ 10
0
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17
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2.8k
views
How to check linear model
modalmatrix limma R linear
2.5 years ago Jitendra ▴ 10
0
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1
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1.2k
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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3
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2.0k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by ▴ 10
1
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2
replies
1.5k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
2.5 years ago abhisek001 • 0
0
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4
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1.6k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.5 years ago Dr. • 0
0
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1
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1.7k
views
Extract Intersection Values from Venn
R Venn
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
2
votes
6
replies
2.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.5 years ago yr542 • 0
0
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0
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857
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.5 years ago Luomeng • 0
2
votes
9
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2.0k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
2
replies
4.5k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.5 years ago by 52k • written 2.6 years ago by • 0
1,163 results • Page 1 of 24
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Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ATpoint ★ 4.9k
No, cells from the same donor are correlated due to the donor effect. There is literature on this you should read to get started. https:/…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by Raya • 0
Wouldn't each sample in the single cell rna seq act as a biological replicate? each condition (eg: mab3_20C) has ~70 single cell samples.
Comment: Getting way too many DEGs with LRT for time-series RNA-seq! by James W. MacDonald 68k
>Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! They are not the…
Comment: Getting way too many DEGs with LRT for time-series RNA-seq! by Denise • 0
Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! And I suppose ther…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ATpoint ★ 4.9k
There is no biological replication here. This is not supported by DESeq2 (or mos credible statistical tools). You would need different dono…
Votes
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Answer: Are voomByGroup and voomLmFit compatible?
Answer: p-adjusted values in multiple comparisons
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