21
votes
24
replies
15k
views
Problem with biomart's listMarts function
biomart bug
updated 9.7 years ago by ▴ 470 • written 10.2 years ago by ★ 2.1k
0
votes
1
reply
1.5k
views
Lumi error in importMethylIDAT
lumi methylation illumina
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
1
vote
4
replies
3.9k
views
Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
9.7 years ago José Luis Lavín ▴ 10
0
votes
2
replies
1.4k
views
MethylPipe pvalue output
MethylPipe
updated 9.7 years ago by ▴ 10 • written 9.7 years ago by • 0
1
vote
2
replies
1.7k
views
Normalized count or Count data for ToPASeq package
rnaseq Topaseq
9.7 years ago saamar.rajput • 0
0
votes
1
reply
923
views
Installing mzMatch - problems with Rcpp versions
software error
updated 9.7 years ago by 25k • written 9.7 years ago by • 0
3
votes
1
reply
1.1k
views
Detection of methylated regions from MeDIP data using csaw
csaw medip-chip
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
0
votes
0
replies
1.8k
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
9.7 years ago Katja Hebestreit ▴ 130
0
votes
3
replies
1.8k
views
biomaRt query Error "no upstream flank found" only for human
biomaRt Query ERROR biomart Filter upstream_flank NOT FOUND
9.7 years ago Ddaubentonia • 0
3
votes
3
replies
1.1k
views
edgeR: shall I fit the glm model separately for different cell lines?
edger
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 20
0
votes
2
replies
1.2k
views
Error in processAmplicons "there are duplicate hairpin sequences"
processamplicons
9.7 years ago lucia.caceres • 0
1
vote
5
replies
1.7k
views
trying to change length of barcode
processamplicons edger barcode
9.7 years ago lucia.caceres • 0
0
votes
2
replies
1.9k
views
volcano plot in Limma
limma volcanoplot
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
6
votes
12
replies
20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
1
vote
0
replies
2.3k
views
HTqPCR readCtData 12 samples x 63 genes - error: row names supplied are of the wrong length
HTqPCR readCtData Heidi Dvinge
9.7 years ago virginia.claudio ▴ 10
0
votes
1
reply
1.3k
views
Installation error GeneRFold and GeneR.
GeneRFold GeneR
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 50
1
vote
3
replies
2.2k
views
DEXSeq warnings for millions of reads
DEXSeq warnings dexseq_count
updated 9.7 years ago by ▴ 130 • written 9.7 years ago by ★ 1.5k
2
votes
5
replies
1.9k
views
Sample code doesn't seem to be working on fresh install of regioneR
regioner
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 140
1
vote
1
reply
1.8k
views
How to get diff expresion results from sam files
differential gene expression sam
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
2
votes
3
replies
3.9k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
9.7 years ago aatsmith • 0
4
votes
2
replies
1.6k
views
Get internal exons using GenomicFeatures
genomicfeatures granges
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 10
4
votes
9
replies
5.8k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.7 years ago Leonardo Collado Torres ★ 1.1k
0
votes
8
replies
2.5k
views
Regarding somatic signature package
somaticsignatures
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 10
5
votes
8
replies
3.3k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 80
1
vote
2
replies
9.0k
views
Error in dyn.load(file, DLLpath = DLLpath, ...) :
R qvalue
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
1
vote
3
replies
1.7k
views
GeneR installation error
GeneR
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 50
0
votes
3
replies
1.6k
views
replace, merge and delete entries in GRangeList
grangeslist
updated 9.7 years ago by ★ 11k • written 9.7 years ago by • 0
1
vote
1
reply
1.5k
views
OpenCyto -- time gate and border events
opencyto gating flowcore flow cytometry
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 30
4
votes
2
replies
2.0k
views
Voom: estimation of mean-variance relationship with gene expression data normalized with methods other than cpm
limma voom
updated 9.7 years ago by 53k • written 9.7 years ago by • 0
3
votes
1
reply
1.8k
views
AnnotationHub: confusing pValue/qValue for (some) Roadmap records
roadmap project annotationhub epigenomics big data
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 350
4
votes
1
reply
3.6k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
0
votes
0
replies
1.1k
views
illumina HM 450 data
illumina450k methylation
9.7 years ago niutster • 0
3
votes
4
replies
2.4k
views
DESeq2::rlog - does it make sense to use it when I don't have duplicates?
deseq2
9.7 years ago Chao-Jen Wong ▴ 40
0
votes
2
replies
3.0k
views
OpenCyto -- proper gating of CD45
opencyto gating flowworkspace
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 30
2
votes
6
replies
2.2k
views
effect of polyploidy level on RUVs normalisation
normalization ruvseq ruvnormalize ruvs eda
9.7 years ago thomas.wolfe • 0
2
votes
8
replies
2.5k
views
edgeR - inconsistent logFC sign
edgeR
9.7 years ago sharvari gujja ▴ 40
1
vote
5
replies
2.9k
views
Gviz AlignmentTrack problem
Gviz
updated 9.7 years ago by ▴ 750 • written 9.7 years ago by • 0
0
votes
4
replies
2.0k
views
problem of GOSemSim R package operation geneSim()
gosemsim
9.7 years ago bnembarekmarwa • 0
1
vote
3
replies
2.1k
views
OpenCyto - getting gate coordinates
opencyto
9.7 years ago Ulrik Stervbo ▴ 30
0
votes
1
reply
1.9k
views
DESeq2 followed by Reporting tools lists blank ensemble gene ID's and symbols but has image, logFC and p-value intact in HTML file
deseq2 rnaseq reportingtools
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
2
votes
5
replies
1.2k
views
a complicate scenario for Design Matrix
edgeR design matrix
updated 9.7 years ago by ★ 29k • written 9.7 years ago by • 0
3
votes
3
replies
2.5k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 9.7 years ago by ★ 13k • written 9.7 years ago by • 0
4
votes
3
replies
3.5k
views
Modifying eset@assayData$exprs : Error : cannot change value of locked binding for 'exprs'
GEOquery
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 40
0
votes
1
reply
1.7k
views
ChipQCSample error Error in `colnames<-`(`*tmp*`, value = c("A", "B", "C")) : length of 'dimnames' [2] not equal to array extent
chipseq chipqc
updated 9.7 years ago by ▴ 420 • written 9.7 years ago by • 0
0
votes
0
replies
1.6k
views
Rjava proxy configuration ?
rJAVA java proxy connectiontimeout rdavidwebservice
9.7 years ago Julien FOURET • 0
0
votes
5
replies
2.3k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
9.7 years ago TimothéeFlutre ▴ 80
0
votes
6
replies
3.5k
views
Help Error could not find function xcmsSet
xcms metabolomics mzr rcpp ramp
9.7 years ago dfrtyu • 0
0
votes
3
replies
1.7k
views
Prevent biocLite() from asking to update packages every time it's used
bioclite package installation package updates
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 40
0
votes
0
replies
1.9k
views
Job: Senior Postdoctoral Fellow in Computational Biology/Bioinformatics : Adelaide, Australia
postdoc bioinformatics network analysis australia systemsbiology Job
9.7 years ago david.lynn • 0
0
votes
3
replies
1.4k
views
VariantAnnotation dbSNPs strand
variantannotation
9.7 years ago ribioinfo ▴ 100
46,719 results • Page 398 of 935
Recent ...
Replies
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
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