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2
votes
1
reply
1.4k
views
biomaRt fails to retrieve GO description for some particular gene
biomart go r bioconductor symbol
6.2 years ago foehn ▴ 100
0
votes
0
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1.1k
views
Sample grouping (phenoData) and visualization in R package- HtqPCR
HtqPCR grouping visualization R phenoData
6.2 years ago mohammedtoufiq91 ▴ 10
2
votes
4
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1.0k
views
Is magrittr "%>%" acceptable in bioc packages?
R bioconductor
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
0
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1.1k
views
Error on labeledHeatmap() function - WGCNA 1.68
WGCNA R
6.2 years ago feltrin88 • 0
1
vote
2
replies
1.0k
views
Using WGCNA for purposes other than RNA-SEQ/Microarray
WGCNA R
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by • 0
0
votes
10
replies
3.2k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error RNAseq tximport R
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
1
reply
2.4k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
6.2 years ago anahochmanova • 0
0
votes
1
reply
1.7k
views
XCMS - cannot allocate vector of size **Gb when global environment is empty
r xcms
6.2 years ago garfield320 ▴ 30
2
votes
4
replies
4.4k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 20 months ago by 53k • written 6.2 years ago by • 0
0
votes
1
reply
2.4k
views
writing gse series matrix data into a csv file
R
6.2 years ago cs18s003 • 0
0
votes
6
replies
1.4k
views
DESeq2: Contrasts in multifactor design with interaction terms
r deseq2
6.2 years ago arielle • 0
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.2 years ago by 53k • written 6.8 years ago by • 0
5
votes
11
replies
4.4k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
6.4 years ago • updated 6.2 years ago pierre.marin • 0
0
votes
2
replies
1.7k
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R ensemblVEP gene annotation Variant Effect Predictor Ensembl VEP
6.2 years ago ycchang • 0
0
votes
7
replies
2.3k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 6.3 years ago by ★ 4.3k • written 6.3 years ago by • 0
2
votes
1
reply
1.3k
views
> DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
DiffBind R R Studio
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 10
0
votes
1
reply
913
views
find genes near a microRNA binding site
R microRNA genes binding Site
6.3 years ago pengu447 • 0
1
vote
2
replies
836
views
Error in biomaRt query - "biomaRt expected a character string of length 1.
biomart R
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by • 0
0
votes
1
reply
1.3k
views
Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt
r
updated 6.3 years ago by ▴ 150 • written 6.3 years ago by • 0
1
vote
3
replies
1.7k
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 20
0
votes
0
replies
883
views
Analyze ct data using HTqPCR
HTqPCR R NormqPCR
6.3 years ago annesha • 0
10
votes
8
replies
4.6k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
6.3 years ago m93 ▴ 10
0
votes
1
reply
922
views
MSGF+ is it possible to specify more than one enzyme for digestion in R?
ms gf plus enzyme R
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by • 0
0
votes
1
reply
6.3k
views
Reordering clusters when plotting pheatmap in R
R pheatmap clusters
6.3 years ago ecg1g15 ▴ 30
0
votes
1
reply
668
views
pakagae sm and package caroline
R caroline sm MASS
6.3 years ago prabin.dm • 0
0
votes
1
reply
1.4k
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
biomart ensembl R Bioconductor
6.3 years ago lbuo • 0
3
votes
3
replies
946
views
Quiery to biomart returned an invalid result
R biomaRt
updated 6.3 years ago by ★ 6.6k • written 6.3 years ago by ▴ 10
0
votes
0
replies
554
views
(R pkg) Pathview Question: How to set node size?
r
6.3 years ago lihe.liu • 0
0
votes
1
reply
1.3k
views
Assesing genomic segment enrichment with GenomicRanges (R-package)
GenomicRanges R genomic enrichment
updated 6.4 years ago by ★ 11k • written 6.4 years ago by • 0
0
votes
15
replies
3.6k
views
Is the STRINGdb server down?
STRINGdb R protein
updated 6.4 years ago by • 0 • written 6.6 years ago by • 0
0
votes
3
replies
1.3k
views
How to find number of patients (percentage of given population) having high expression of gene A in given microarray data ?
microarray r clustering high expressed genes
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
2
votes
1
reply
2.1k
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
6.4 years ago epibio ▴ 10
2
votes
2
replies
3.6k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
0
votes
9
replies
2.1k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
votes
1
reply
693
views
how to remove row which value were found in group before
GenomicRanges r
6.4 years ago naktang1 • 0
0
votes
6
replies
2.2k
views
Plot genes with similar expression patterns
deseq2 R RNASeq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
2
votes
4
replies
6.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
1
vote
6
replies
2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 120
4
votes
3
replies
4.2k
views
Align legends to each heatmap in a ComplexHeatmap with 2 heatmaps
complexheatmap r
updated 6.4 years ago by ▴ 290 • written 6.4 years ago by ▴ 220
0
votes
3
replies
2.6k
views
Change order of conditions when plotting: plotCounts {DESeq2}
R deseq2 plotcounts
6.4 years ago ecg1g15 ▴ 30
8
votes
5
replies
4.9k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 120
1
vote
2
replies
1.6k
views
What is the '?' in the result of R package 'msa' function 'msa'?
MSA R Multiple sequence alignment consensus sequence
updated 6.4 years ago by ▴ 20 • written 6.4 years ago by • 0
0
votes
2
replies
1.3k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger r differentialanalysis rnaseq designmatrix
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
7
votes
9
replies
6.0k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.7 years ago by ★ 3.0k • written 6.5 years ago by ▴ 10
0
votes
1
reply
1.4k
views
WGCNA::modulePreservation - Error in make.unique(rownames(datRef)) : 'names' must be a character vector
R WGCNA
6.5 years ago Alex Nesmelov • 0
0
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0
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1.2k
views
How are the MotifbreakR scores calculated, and how do they relate to one another?
MotifbreakR R motifs
6.5 years ago camerond • 0
1
vote
2
replies
1.6k
views
biomaRt fails to get flanking sequence
biomaRt software error R
updated 13 months ago by • 0 • written 6.5 years ago by • 0
1
vote
3
replies
523
views
Hello All can any one please help?
microarray bioconductor R
6.5 years ago sumode • 0
0
votes
1
reply
1.1k
views
DESeq2 Design for 2 Conditions
deseq2 r R RNA-Seq
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
3
replies
1.7k
views
How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
1,163 results • Page 8 of 24
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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