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0
votes
2
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11k
views
Add selected row names on pheatmap
R pheatmap
updated 5.0 years ago by ★ 5.0k • written 5.0 years ago by ▴ 30
7
votes
6
replies
5.1k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
5.0 years ago ecg1g15 ▴ 30
9
votes
5
replies
5.2k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
5.0 years ago ecg1g15 ▴ 30
0
votes
0
replies
1.3k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
5.0 years ago • updated 4.7 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.2k
views
I am using the DEP package example dataset, and I am getting this error on: plot_frequency(data_se)
DEP R Bioconductor Plot
updated 5.1 years ago by 4.2k • written 5.1 years ago by • 0
0
votes
3
replies
4.0k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode : logical
R DESeq2
5.1 years ago Ricard Lambea • 0
2
votes
6
replies
3.1k
views
Cannot download “EBImage” library in R
R EBImage
written 5.1 years ago by • 0
0
votes
0
replies
1.4k
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
5.1 years ago mmartin ▴ 20
0
votes
1
reply
1.4k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
votes
4
replies
1.7k
views
Bioconductor package development
package R software development
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
1
vote
6
replies
2.2k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
2
replies
1.6k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
5.2 years ago Marco_aurelio • 0
0
votes
0
replies
848
views
plots in gwasurvivr
gwasurvivr r survival cox
5.2 years ago laura.martinez.campelo • 0
0
votes
2
replies
2.5k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
3
votes
16
replies
6.3k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 4.1 years ago by ▴ 10 • written 5.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
K Means Clustering Two Matrices for ComplexHeatmap
complexheatmap R
5.2 years ago pthom010 • 0
2
votes
6
replies
4.6k
views
Can't install package oligoClasses
R oligoClasses ff
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 20
3
votes
1
reply
1.2k
views
Create a '.db' package for agilent
R agilent microarray
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 20
0
votes
2
replies
1.1k
views
How to normalise data in ballgown?
r normalization edger
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
5
votes
8
replies
2.4k
views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
updated 5.3 years ago by ▴ 220 • written 5.3 years ago by ▴ 10
1
vote
4
replies
2.5k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Differential gene expression using Ballgown
r normalization
5.3 years ago lakshmi9c • 0
0
votes
4
replies
3.0k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by • 0
0
votes
1
reply
1.1k
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 20
2
votes
5
replies
1.6k
views
the results from normalized=TRUE and normalized = FALSE is the same
R deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
3
replies
2.0k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.3 years ago TriS ▴ 200
0
votes
2
replies
1.8k
views
Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 40
0
votes
3
replies
1.5k
views
Use topGOdata in devtools package
topGO devtools R
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
2
votes
1
reply
3.3k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 60
2
votes
4
replies
12k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 60
6
votes
11
replies
2.8k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 5.3 years ago by ★ 6.6k • written 5.3 years ago by • 0
2
votes
3
replies
1.3k
views
Annotation of Genomic Regions
annotation genomic regions R
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
1
vote
4
replies
1.5k
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
5.3 years ago Arpi Beshlikyan • 0
2
votes
1
reply
819
views
diffbind from own binding affinity table
diffbind R
updated 5.3 years ago by ★ 5.2k • written 5.3 years ago by • 0
0
votes
7
replies
2.1k
views
WGCNA to Cytoscape error
R
5.4 years ago zen • 0
0
votes
6
replies
2.1k
views
Error when trying to access BiomaRt from a cluster
biomaRt R cluster
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
0
votes
1
reply
988
views
?? Any R script for subtracting multiple controls from multiple patients in data.frame and assign 1 if output is less than 0
Rscript data.frame forloop R
5.4 years ago Ankit ▴ 20
0
votes
2
replies
1.6k
views
EGAD R-package: How to generate a 2-column matrix with gene-interactions required for "make_annotations()"-function?
EGAD_1.16.0 EGAD R network analysis
updated 3.7 years ago by • 0 • written 5.4 years ago by • 0
0
votes
5
replies
1.7k
views
DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
1
reply
1.2k
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 5.0 years ago by ▴ 30 • written 5.4 years ago by • 0
3
votes
3
replies
1.7k
views
How can I use 'geom_taxalink()' with the circular layout in the 'ggtree' package in R?
r ggtree phylogeny
updated 5.4 years ago by ★ 1.2k • written 5.4 years ago by ▴ 10
1
vote
3
replies
3.6k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 2.8 years ago by ★ 4.0k • written 5.4 years ago by • 0
0
votes
0
replies
2.3k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
genomics NGS R genetics statistics
7.4 years ago • updated 5.0 years ago Luo Weijun ★ 1.6k
0
votes
8
replies
1.3k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
2
replies
1.9k
views
"Error in nbinomLRT(... less than one degree of freedom"... Isolating main and interaction effects with the LRT?
deseq2 main effects interaction effects R lrt
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
12
replies
2.0k
views
Taking much longer time for same script after R upgrade to 4.0
R
5.5 years ago hsiowa2 ▴ 20
3
votes
5
replies
1.2k
views
How to loop over two files ...and calculate R^2 between SNPs
loops R
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
0
votes
9
replies
2.5k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.5 years ago camillab. ▴ 10
1
vote
0
replies
1.6k
views
Job: Bioinformatics Data Analyst
R RNA-seq job Job
5.5 years ago António Miguel de Jesus Domingues ▴ 510
1
vote
3
replies
933
views
Use Tx2Gene for Annotation
deseq2 annotation r
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1,163 results • Page 5 of 24
Recent ...
Replies
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…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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