Showing : r • reset
2
votes
3
replies
260
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 days ago by • 0
3
votes
3
replies
14k
views
How to fix 'long vectors not supported yet' error in R
r
updated 3 months ago by • 0 • written 5.4 years ago by • 0
0
votes
0
replies
200
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
4 months ago danalvoronov ▴ 10
0
votes
4
replies
501
views
limma with interaction term
R biostatistics limma Epigenetics
5 months ago Jitendra ▴ 10
0
votes
3
replies
1.8k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.4 years ago by • 0
1
vote
5
replies
2.3k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.5 years ago by ▴ 10
0
votes
3
replies
676
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
0
replies
327
views
multipollutant models
statistics Regression r limma
8 months ago Jitendra ▴ 10
3
votes
4
replies
675
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
8 months ago pl23 • 0
1
vote
3
replies
1.6k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 8 months ago by ▴ 740 • written 3.2 years ago by • 0
0
votes
10
replies
1.0k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
8 months ago • updated 4 months ago ScafioRuo • 0
12
votes
10
replies
9.3k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 4 months ago by • 0 • written 9 months ago by ▴ 20
0
votes
2
replies
671
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
11 months ago • updated 10 months ago yr542 • 0
1
vote
2
replies
762
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
12 months ago Miguel • 0
2
votes
5
replies
1.5k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
12 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
597
views
Gene enrichment analysis
analysis R GOfuncR
updated 13 months ago by ▴ 730 • written 13 months ago by • 0
0
votes
2
replies
1.3k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 14 months ago by • 0 • written 3.4 years ago by • 0
0
votes
1
reply
711
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 15 months ago by 51k • written 15 months ago by • 0
0
votes
1
reply
582
views
DEseq2 Single cell data paired design
R
updated 15 months ago by ▴ 30 • written 15 months ago by • 0
0
votes
4
replies
1.1k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
vote
3
replies
1.0k
views
tximport error
tximport r
updated 15 months ago by 42k • written 15 months ago by • 0
1
vote
2
replies
1.0k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
15 months ago Abdul ▴ 20
0
votes
0
replies
544
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
15 months ago aymanreffai • 0
1
vote
1
reply
1.5k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 10
0
votes
4
replies
1.0k
views
Unable to install BiocManager
Biocmanager R
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
1
vote
1
reply
1.4k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 16 months ago by • 0 • written 16 months ago by • 0
0
votes
13
replies
6.0k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
16 months ago Laia ▴ 10
1
vote
3
replies
4.8k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 16 months ago by ★ 4.0k • written 17 months ago by ▴ 10
0
votes
1
reply
878
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 16 months ago by ▴ 740 • written 16 months ago by ▴ 10
0
votes
0
replies
556
views
rDGIdb package: score of the results
rDGIdb r
16 months ago HELEN • 0
2
votes
1
reply
576
views
add column with name in R
name R column
updated 16 months ago by ▴ 70 • written 16 months ago by • 0
0
votes
4
replies
1.0k
views
how to extract list in quantile in R
R quantile list
16 months ago sat • 0
0
votes
0
replies
686
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
16 months ago Manav • 0
0
votes
0
replies
637
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
17 months ago Jitendra ▴ 10
3
votes
2
replies
943
views
how to extract and match information of two filein R
R column match
17 months ago sat • 0
0
votes
0
replies
587
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
17 months ago info ▴ 10
0
votes
17
replies
1.9k
views
How to check linear model
modalmatrix limma R linear
17 months ago Jitendra ▴ 10
0
votes
1
reply
812
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 17 months ago by 66k • written 17 months ago by • 0
0
votes
3
replies
1.2k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 17 months ago by ▴ 730 • written 17 months ago by ▴ 10
1
vote
2
replies
956
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
17 months ago abhisek001 • 0
0
votes
4
replies
1.1k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
17 months ago Dr. • 0
0
votes
1
reply
1.1k
views
Extract Intersection Values from Venn
R Venn
updated 17 months ago by 66k • written 17 months ago by • 0
2
votes
6
replies
1.9k
views
DMRcate
DMRcate R DMRcatedata Markdown
17 months ago yr542 • 0
0
votes
0
replies
606
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
17 months ago Luomeng • 0
2
votes
9
replies
1.4k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 17 months ago by 66k • written 17 months ago by • 0
1
vote
2
replies
2.4k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 17 months ago by 51k • written 18 months ago by • 0
0
votes
3
replies
1.1k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 18 months ago by 66k • written 18 months ago by • 0
0
votes
1
reply
713
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 18 months ago by 51k • written 18 months ago by • 0
0
votes
2
replies
833
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 19 months ago by • 0 • written 20 months ago by ▴ 90
2
votes
4
replies
2.4k
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 20 months ago by • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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