Showing : r • reset
2
votes
1
reply
1.4k
views
biomaRt fails to retrieve GO description for some particular gene
biomart go r bioconductor symbol
6.3 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
6.3 years ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
1.1k
views
Is magrittr "%>%" acceptable in bioc packages?
R bioconductor
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
0
votes
0
replies
1.1k
views
Error on labeledHeatmap() function - WGCNA 1.68
WGCNA R
6.3 years ago feltrin88 • 0
1
vote
2
replies
1.1k
views
Using WGCNA for purposes other than RNA-SEQ/Microarray
WGCNA R
updated 6.3 years ago by ★ 3.0k • written 6.3 years ago by • 0
0
votes
10
replies
3.3k
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 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
1
reply
2.5k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
6.4 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
6.4 years ago garfield320 ▴ 30
2
votes
4
replies
4.5k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 22 months ago by 53k • written 6.4 years ago by • 0
0
votes
1
reply
2.5k
views
writing gse series matrix data into a csv file
R
6.4 years ago cs18s003 • 0
0
votes
6
replies
1.5k
views
DESeq2: Contrasts in multifactor design with interaction terms
r deseq2
6.4 years ago arielle • 0
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.4 years ago by 53k • written 7.0 years ago by • 0
5
votes
11
replies
4.5k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
6.5 years ago • updated 6.4 years ago pierre.marin • 0
0
votes
2
replies
1.8k
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R ensemblVEP gene annotation Variant Effect Predictor Ensembl VEP
6.4 years ago ycchang • 0
0
votes
7
replies
2.4k
views
ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
ATACseqQC R
updated 6.4 years ago by ★ 4.3k • written 6.4 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 6.4 years ago by 68k • written 6.4 years ago by ▴ 10
0
votes
1
reply
981
views
find genes near a microRNA binding site
R microRNA genes binding Site
6.4 years ago pengu447 • 0
1
vote
2
replies
882
views
Error in biomaRt query - "biomaRt expected a character string of length 1.
biomart R
updated 6.4 years ago by ▴ 10 • written 6.4 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 6.4 years ago by ▴ 150 • written 6.4 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 6.4 years ago by 25k • written 6.4 years ago by ▴ 20
0
votes
0
replies
934
views
Analyze ct data using HTqPCR
HTqPCR R NormqPCR
6.4 years ago annesha • 0
10
votes
8
replies
4.7k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
6.4 years ago m93 ▴ 10
0
votes
1
reply
973
views
MSGF+ is it possible to specify more than one enzyme for digestion in R?
ms gf plus enzyme R
updated 6.4 years ago by ▴ 70 • written 6.4 years ago by • 0
0
votes
1
reply
6.5k
views
Reordering clusters when plotting pheatmap in R
R pheatmap clusters
6.5 years ago ecg1g15 ▴ 30
0
votes
1
reply
696
views
pakagae sm and package caroline
R caroline sm MASS
6.5 years ago prabin.dm • 0
0
votes
1
reply
1.5k
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
biomart ensembl R Bioconductor
6.5 years ago lbuo • 0
3
votes
3
replies
985
views
Quiery to biomart returned an invalid result
R biomaRt
updated 6.5 years ago by ★ 6.6k • written 6.5 years ago by ▴ 10
0
votes
0
replies
579
views
(R pkg) Pathview Question: How to set node size?
r
6.5 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 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
votes
15
replies
3.7k
views
Is the STRINGdb server down?
STRINGdb R protein
updated 6.5 years ago by • 0 • written 6.7 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 6.5 years ago by 68k • written 6.5 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
6.5 years ago epibio ▴ 10
2
votes
2
replies
3.7k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by ▴ 10
0
votes
9
replies
2.1k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
1
reply
723
views
how to remove row which value were found in group before
GenomicRanges r
6.6 years ago naktang1 • 0
0
votes
6
replies
2.3k
views
Plot genes with similar expression patterns
deseq2 R RNASeq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
2
votes
4
replies
6.1k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
vote
6
replies
2.4k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 120
4
votes
3
replies
4.3k
views
Align legends to each heatmap in a ComplexHeatmap with 2 heatmaps
complexheatmap r
updated 6.6 years ago by ▴ 290 • written 6.6 years ago by ▴ 220
0
votes
3
replies
2.6k
views
Change order of conditions when plotting: plotCounts {DESeq2}
R deseq2 plotcounts
6.6 years ago ecg1g15 ▴ 30
8
votes
5
replies
5.1k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 120
1
vote
2
replies
1.7k
views
What is the '?' in the result of R package 'msa' function 'msa'?
MSA R Multiple sequence alignment consensus sequence
updated 6.6 years ago by ▴ 20 • written 6.6 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 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 60
7
votes
9
replies
6.2k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.9 years ago by ★ 3.0k • written 6.6 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
6.6 years ago Alex Nesmelov • 0
0
votes
0
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1.3k
views
How are the MotifbreakR scores calculated, and how do they relate to one another?
MotifbreakR R motifs
6.6 years ago camerond • 0
1
vote
2
replies
1.6k
views
biomaRt fails to get flanking sequence
biomaRt software error R
updated 15 months ago by • 0 • written 6.6 years ago by • 0
1
vote
3
replies
549
views
Hello All can any one please help?
microarray bioconductor R
6.6 years ago sumode • 0
0
votes
1
reply
1.2k
views
DESeq2 Design for 2 Conditions
deseq2 r R RNA-Seq
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
3
replies
1.8k
views
How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1,163 results • Page 8 of 24
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Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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