Showing : R • reset
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 23 days ago by • 0 • written 5.2 years ago by • 0
0
votes
0
replies
110
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
8 weeks ago danalvoronov ▴ 10
0
votes
4
replies
347
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 8 weeks ago Jitendra ▴ 10
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.2 years ago by • 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
0
votes
3
replies
478
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
220
views
multipollutant models
statistics Regression r limma
5 months ago Jitendra ▴ 10
3
votes
4
replies
521
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
0
votes
10
replies
796
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
5 months ago • updated 8 weeks ago ScafioRuo • 0
10
votes
10
replies
6.7k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 5 weeks ago by • 0 • written 6 months ago by ▴ 10
0
votes
2
replies
546
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
1
vote
2
replies
593
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
9 months ago Miguel • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
508
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 11 months ago by • 0 • written 3.2 years ago by • 0
0
votes
1
reply
627
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
1
reply
494
views
DEseq2 Single cell data paired design
R
updated 12 months ago by ▴ 30 • written 12 months ago by • 0
0
votes
4
replies
887
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
1
vote
3
replies
854
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
1
vote
2
replies
878
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
0
votes
0
replies
479
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
1
vote
1
reply
1.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
0
votes
4
replies
873
views
Unable to install BiocManager
Biocmanager R
updated 12 months ago by ▴ 50 • written 12 months ago by • 0
1
vote
1
reply
1.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 13 months ago by • 0 • written 13 months ago by • 0
0
votes
13
replies
4.7k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
0
votes
3
replies
3.8k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 13 months ago by ★ 3.9k • written 14 months ago by • 0
0
votes
1
reply
721
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
0
votes
0
replies
464
views
rDGIdb package: score of the results
rDGIdb r
13 months ago HELEN • 0
2
votes
1
reply
514
views
add column with name in R
name R column
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
0
votes
4
replies
859
views
how to extract list in quantile in R
R quantile list
13 months ago sat • 0
0
votes
0
replies
540
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
13 months ago Manav • 0
0
votes
0
replies
555
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
14 months ago Jitendra ▴ 10
3
votes
2
replies
794
views
how to extract and match information of two filein R
R column match
14 months ago sat • 0
0
votes
0
replies
502
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
14 months ago info ▴ 10
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix limma R linear
14 months ago Jitendra ▴ 10
0
votes
1
reply
732
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
3
replies
937
views
batch effect in EPIC array data
statistics Epigenetics R
updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
1
vote
2
replies
833
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
14 months ago abhisek001 • 0
0
votes
4
replies
945
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
14 months ago Dr. • 0
0
votes
1
reply
871
views
Extract Intersection Values from Venn
R Venn
updated 14 months ago by 65k • written 14 months ago by • 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
14 months ago yr542 • 0
0
votes
0
replies
530
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
14 months ago Luomeng • 0
2
votes
9
replies
1.2k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
2
replies
1.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 14 months ago by 50k • written 15 months ago by • 0
0
votes
3
replies
918
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
640
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 15 months ago by 50k • written 15 months ago by • 0
0
votes
2
replies
714
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 16 months ago by • 0 • written 17 months ago by ▴ 90
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 17 months ago by • 0
0
votes
1
reply
661
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 16 months ago by 41k • written 16 months ago by • 0
50 results • Page 1 of 1
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Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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