Showing : r • reset
9
votes
7
replies
5.5k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 6.9 years ago by ▴ 30 • written 7.0 years ago by ▴ 50
1
vote
2
replies
1.7k
views
an error in the Venn Diagram creating
R software error
6.9 years ago morteza.hadizade ▴ 10
0
votes
1
reply
1.5k
views
What is the name of this probe?
affymetrix microarrays hta20transcriptcluster r select
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
5
votes
1
reply
6.0k
views
RNAseq analysis: what comes first, filtering or normalization
edger R rnaseq
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 30
0
votes
0
replies
1.2k
views
ASpli AsDiscover error
R alternative splicing ASpli AsDiscover
7.0 years ago abdul rawoof ▴ 60
0
votes
0
replies
917
views
Error in base::strsplit(x, ...) : non-character argument
software error r readComp {systemPipeR}
7.0 years ago catscampos • 0
4
votes
2
replies
1.6k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
7.0 years ago foehn ▴ 100
0
votes
0
replies
1.2k
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
7.0 years ago Ramiro Magno ▴ 100
3
votes
5
replies
1.9k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
0
votes
2
replies
3.9k
views
Problem installing scater
scater R biocmanager bioconductor
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
2
votes
4
replies
2.6k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 2.7 years ago by ▴ 10 • written 7.0 years ago by • 0
3
votes
6
replies
2.9k
views
Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 7.0 years ago by ▴ 280 • written 7.0 years ago by • 0
0
votes
3
replies
1.7k
views
Installing lpsymphony on Mac OS X
R lpsymphony mac os x
updated 7.0 years ago by ★ 13k • written 7.1 years ago by • 0
0
votes
2
replies
1.5k
views
Rsubread installation failed
r package installation
7.1 years ago justinkablan225 ▴ 10
0
votes
1
reply
1.5k
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 7.1 years ago by ★ 2.1k • written 7.1 years ago by • 0
1
vote
5
replies
1.5k
views
Biomart cannot get multiple genes?
R biomart
7.1 years ago Mike ▴ 10
1
vote
4
replies
1.9k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 2.7 years ago by 53k • written 7.1 years ago by ▴ 10
0
votes
3
replies
5.6k
views
Rhdf5lib install problems
R bioconductor rhdf5 biocmanager 3.5
7.1 years ago cem45 • 0
0
votes
1
reply
3.8k
views
Timeout was reached error in GEOquery package
R microarray software error
updated 7.1 years ago by ★ 4.0k • written 7.1 years ago by ▴ 10
0
votes
2
replies
2.6k
views
Please help with workspace error in R
R test fisher exact workspace
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 20
8
votes
4
replies
1.6k
views
maintainer option for bioconductor packages
bioconductor R
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 70
1
vote
2
replies
2.0k
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
7.1 years ago DMA1 ▴ 10
3
votes
2
replies
2.8k
views
biomaRt question (missing gene information?)
biomart R
updated 7.1 years ago by ★ 6.6k • written 7.1 years ago by ▴ 10
0
votes
5
replies
3.6k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R annotation ensembldb
7.1 years ago foehn ▴ 100
0
votes
1
reply
1.9k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 2.6 years ago by • 0 • written 7.1 years ago by • 0
1
vote
2
replies
946
views
Dispersion & FDR in edgeR
edger R
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
2
votes
4
replies
5.0k
views
Error in windows() function
software error R windows
updated 7.2 years ago by ★ 6.6k • written 7.2 years ago by • 0
7
votes
7
replies
2.3k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 7.2 years ago by 21k • written 7.2 years ago by ▴ 50
3
votes
3
replies
1.9k
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by • 0
1
vote
1
reply
1.2k
views
Job: Software Development Engineer at Fred Hutch (Seattle, WA)
job software engineer R Job
7.2 years ago jkim2345 ▴ 10
0
votes
4
replies
1.3k
views
how to make gene cluster from RNA-Seq counts?
deseq2 rnaseq R
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
3
votes
4
replies
1.9k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 7.2 years ago by ▴ 80 • written 7.2 years ago by • 0
0
votes
3
replies
1.4k
views
Creation of qPCRset in R for HtqPCR
R bioconductor htqpcr qpcrset object
7.2 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
1.1k
views
R script to fix the error in dataframe when using ballgown for differentially expression analysis
r ballgown code error
7.2 years ago amy16 • 0
0
votes
0
replies
1.2k
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
7.2 years ago pierre.marin • 0
2
votes
5
replies
14k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
1
vote
1
reply
1.4k
views
ggbio labels with ggrepeal on circos plot
ggbio r graphics
7.2 years ago gamma.jian ▴ 10
2
votes
6
replies
3.2k
views
extracting the genes associated with the groups or samples in pheatmap.
R microarray
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
0
votes
3
replies
3.4k
views
Selecting columns form a list of grange objects
r granges grange
7.2 years ago g.k • 0
0
votes
1
reply
1.2k
views
What is the latest version of R that bioimagetools will run on?
r bioimagetools ebimage
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
0
votes
1
reply
1.2k
views
WGCNA tree creation
bioinformatics R
7.2 years ago anjanaram1 ▴ 10
0
votes
1
reply
3.7k
views
How can I create a mean ROC curve for multiple plotted ROC curves, R
R ROC mean plot multiple roc curves
updated 7.2 years ago by ▴ 420 • written 7.2 years ago by • 0
0
votes
7
replies
2.3k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 7.2 years ago by ★ 1.3k • written 7.2 years ago by • 0
2
votes
2
replies
5.2k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
0
replies
1.1k
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
7.2 years ago mtkk94 • 0
3
votes
2
replies
1.7k
views
error when I use groHMM on data outside of the tutorial
grohmm groseq next-generation sequencing R
7.3 years ago Deleted ▴ 70
0
votes
2
replies
1.8k
views
Getting error in running maser 0.99.16
maser R rMATs alternative splicing
7.3 years ago Reza • 0
1
vote
7
replies
1.8k
views
How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edgeR R differential gene expression up-regulation gene list
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
3
votes
3
replies
5.1k
views
Why does biomart work on humans and not mouse genes for HGNC symbol conversion?
biomart r homologue
updated 7.3 years ago by ★ 1.4k • written 7.3 years ago by • 0
0
votes
0
replies
1.6k
views
Match peptide within protein sequence fasta and extract position information based on protein sequence
R seqinr biostrings
7.3 years ago rabalski • 0
1,163 results • Page 10 of 24
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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…
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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