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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 9 months ago by ▴ 10
0
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0
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368
views
[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
754
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 12 months ago by 68k • written 12 months ago by • 0
2
votes
3
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854
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
views
How to fix 'long vectors not supported yet' error in R
r
updated 17 months ago by • 0 • written 6.5 years ago by • 0
0
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0
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476
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
18 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
19 months ago • updated 18 months ago Jitendra ▴ 10
0
votes
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
vote
5
replies
2.7k
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pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.6 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
written 21 months ago by • 0
0
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0
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625
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 18 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
2.1 years ago • updated 24 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
votes
1
reply
933
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
1.9k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 2.3 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
839
views
DEseq2 Single cell data paired design
R
updated 2.4 years ago by ▴ 30 • written 2.4 years ago by • 0
0
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4
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1.6k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
1
vote
3
replies
1.5k
views
tximport error
tximport r
updated 2.4 years ago by 43k • written 2.4 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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863
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
replies
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 2.5 years ago by • 0
0
votes
13
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13k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.4 years ago Laia ▴ 10
1
vote
3
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8.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 2.5 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 2.5 years ago by ▴ 760 • written 2.5 years ago by ▴ 10
0
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0
replies
812
views
rDGIdb package: score of the results
rDGIdb r
2.5 years ago HELEN • 0
2
votes
1
reply
834
views
add column with name in R
name R column
updated 2.5 years ago by ▴ 70 • written 2.5 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
replies
990
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
2.5 years ago Jitendra ▴ 10
3
votes
2
replies
1.5k
views
how to extract and match information of two filein R
R column match
2.5 years ago sat • 0
0
votes
0
replies
907
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.5 years ago info ▴ 10
0
votes
17
replies
2.8k
views
How to check linear model
modalmatrix limma R linear
2.5 years ago Jitendra ▴ 10
0
votes
1
reply
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
votes
3
replies
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
vote
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
votes
4
replies
1.6k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.6 years ago • updated 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 2.6 years ago by 68k • written 2.6 years ago by • 0
2
votes
6
replies
2.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.6 years ago yr542 • 0
0
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0
replies
862
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.6 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 2.6 years ago by 68k • written 2.6 years ago by • 0
1
vote
2
replies
4.6k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
1,163 results • Page 1 of 24
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Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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