Showing : R • reset
1
vote
1
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229
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 11 days ago by 67k • written 13 days ago by • 0
2
votes
3
replies
442
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 weeks ago by • 0
3
votes
3
replies
14k
views
How to fix 'long vectors not supported yet' error in R
r
updated 5 months ago by • 0 • written 5.6 years ago by • 0
0
votes
0
replies
255
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
6 months ago danalvoronov ▴ 10
0
votes
4
replies
595
views
limma with interaction term
R biostatistics limma Epigenetics
7 months ago • updated 6 months ago Jitendra ▴ 10
0
votes
3
replies
1.9k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.5 years ago by • 0
1
vote
5
replies
2.4k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.6 years ago by ▴ 10
0
votes
3
replies
816
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 9 months ago by • 0 • written 9 months ago by • 0
0
votes
0
replies
412
views
multipollutant models
statistics Regression r limma
9 months ago Jitendra ▴ 10
3
votes
4
replies
794
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
9 months ago pl23 • 0
1
vote
3
replies
1.7k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 10 months ago by ▴ 750 • written 3.4 years ago by • 0
0
votes
10
replies
1.1k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
10 months ago • updated 6 months ago ScafioRuo • 0
12
votes
10
replies
10k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 5 months ago by • 0 • written 10 months ago by ▴ 20
0
votes
2
replies
755
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
13 months ago • updated 12 months ago yr542 • 0
1
vote
2
replies
849
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
13 months ago Miguel • 0
2
votes
5
replies
1.6k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
14 months ago • updated 13 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
671
views
Gene enrichment analysis
analysis R GOfuncR
updated 15 months ago by ▴ 730 • written 15 months ago by • 0
0
votes
2
replies
1.4k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 15 months ago by • 0 • written 3.6 years ago by • 0
0
votes
1
reply
784
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 16 months ago by 51k • written 16 months ago by • 0
0
votes
1
reply
629
views
DEseq2 Single cell data paired design
R
updated 16 months ago by ▴ 30 • written 16 months ago by • 0
0
votes
4
replies
1.2k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
1
vote
3
replies
1.1k
views
tximport error
tximport r
updated 17 months ago by 42k • written 17 months ago by • 0
1
vote
2
replies
1.1k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
17 months ago Abdul ▴ 20
0
votes
0
replies
613
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
17 months ago aymanreffai • 0
1
vote
1
reply
1.7k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
0
votes
4
replies
1.1k
views
Unable to install BiocManager
Biocmanager R
updated 17 months ago by ▴ 50 • written 17 months ago by • 0
1
vote
1
reply
1.6k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 17 months ago by • 0 • written 18 months ago by • 0
0
votes
13
replies
6.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
18 months ago Laia ▴ 10
1
vote
3
replies
5.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 18 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
votes
1
reply
975
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 18 months ago by ▴ 740 • written 18 months ago by ▴ 10
0
votes
0
replies
602
views
rDGIdb package: score of the results
rDGIdb r
18 months ago HELEN • 0
2
votes
1
reply
622
views
add column with name in R
name R column
updated 18 months ago by ▴ 70 • written 18 months ago by • 0
0
votes
4
replies
1.1k
views
how to extract list in quantile in R
R quantile list
18 months ago sat • 0
0
votes
0
replies
763
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
18 months ago Manav • 0
0
votes
0
replies
687
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
18 months ago Jitendra ▴ 10
3
votes
2
replies
1.0k
views
how to extract and match information of two filein R
R column match
18 months ago sat • 0
0
votes
0
replies
639
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
18 months ago info ▴ 10
0
votes
17
replies
2.0k
views
How to check linear model
modalmatrix limma R linear
19 months ago • updated 18 months ago Jitendra ▴ 10
0
votes
1
reply
881
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 19 months ago by 67k • written 19 months ago by • 0
0
votes
3
replies
1.3k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 19 months ago by ▴ 730 • written 19 months ago by ▴ 10
1
vote
2
replies
1.0k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
19 months ago abhisek001 • 0
0
votes
4
replies
1.2k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
19 months ago Dr. • 0
0
votes
1
reply
1.2k
views
Extract Intersection Values from Venn
R Venn
updated 19 months ago by 67k • written 19 months ago by • 0
2
votes
6
replies
2.0k
views
DMRcate
DMRcate R DMRcatedata Markdown
19 months ago yr542 • 0
0
votes
0
replies
649
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
19 months ago Luomeng • 0
2
votes
9
replies
1.5k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 19 months ago by 67k • written 19 months ago by • 0
1
vote
2
replies
2.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 19 months ago by 51k • written 20 months ago by • 0
0
votes
3
replies
1.2k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
1
reply
762
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 20 months ago by 51k • written 20 months ago by • 0
0
votes
2
replies
906
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 21 months ago by • 0 • written 22 months ago by ▴ 90
50 results • Page 1 of 1
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Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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