Showing : r • reset
1
vote
1
reply
312
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 25 days ago by 67k • written 27 days ago by • 0
2
votes
3
replies
467
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 10 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
261
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
7 months ago danalvoronov ▴ 10
0
votes
4
replies
609
views
limma with interaction term
R biostatistics limma Epigenetics
7 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 3.6 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
847
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
423
views
multipollutant models
statistics Regression r limma
10 months ago Jitendra ▴ 10
3
votes
4
replies
824
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
10 months ago pl23 • 0
1
vote
3
replies
1.8k
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
1.2k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
10 months ago • updated 7 months ago ScafioRuo • 0
12
votes
10
replies
11k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 6 months ago by • 0 • written 11 months ago by ▴ 20
0
votes
2
replies
769
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
867
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
14 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 mohammedtoufiq91 ▴ 10
0
votes
1
reply
682
views
Gene enrichment analysis
analysis R GOfuncR
updated 15 months ago by ▴ 750 • written 15 months ago by • 0
0
votes
2
replies
1.4k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 16 months ago by • 0 • written 3.6 years ago by • 0
0
votes
1
reply
797
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 17 months ago by 51k • written 17 months ago by • 0
0
votes
1
reply
648
views
DEseq2 Single cell data paired design
R
updated 17 months ago by ▴ 30 • written 17 months ago by • 0
0
votes
4
replies
1.2k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 17 months ago by ★ 1.4k • written 17 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
625
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 18 months ago by • 0 • written 18 months ago by • 0
0
votes
13
replies
6.7k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
18 months ago Laia ▴ 10
1
vote
3
replies
5.4k
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
993
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
613
views
rDGIdb package: score of the results
rDGIdb r
18 months ago HELEN • 0
2
votes
1
reply
631
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
1.2k
views
how to extract list in quantile in R
R quantile list
19 months ago • updated 18 months ago sat • 0
0
votes
0
replies
787
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
19 months ago Manav • 0
0
votes
0
replies
696
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
19 months ago Jitendra ▴ 10
3
votes
2
replies
1.0k
views
how to extract and match information of two filein R
R column match
19 months ago sat • 0
0
votes
0
replies
655
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
19 months ago info ▴ 10
0
votes
17
replies
2.1k
views
How to check linear model
modalmatrix limma R linear
19 months ago Jitendra ▴ 10
0
votes
1
reply
908
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
1.4k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 19 months ago by ▴ 750 • 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
2.1k
views
DMRcate
DMRcate R DMRcatedata Markdown
19 months ago yr542 • 0
0
votes
0
replies
664
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
20 months ago Luomeng • 0
2
votes
9
replies
1.5k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 20 months ago by 67k • written 20 months ago by • 0
1
vote
2
replies
2.8k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 20 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
775
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 21 months ago by • 0
0
votes
2
replies
917
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
Recent ...
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Answer: Poor dispersion fit in DESeq2 by Michael Love 42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p by Michael Love 42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group by Michael Love 42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
Answer: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat by Laurent Gatto 1.6k
Tthis happens because the sequence spectraVariable is expected to be an atomic vector or a List with elements of length 1, but it's not - s…
Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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