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0
votes
2
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12k
views
Add selected row names on pheatmap
R pheatmap
updated 5.2 years ago by ★ 5.0k • written 5.2 years ago by ▴ 30
7
votes
6
replies
5.4k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
5.3 years ago • updated 5.2 years ago ecg1g15 ▴ 30
10
votes
5
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5.9k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
5.3 years ago ecg1g15 ▴ 30
0
votes
0
replies
1.3k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
5.3 years ago • updated 4.9 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.3k
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 5.3 years ago by 4.3k • written 5.3 years ago by • 0
0
votes
3
replies
4.2k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode : logical
R DESeq2
5.3 years ago Ricard Lambea • 0
2
votes
6
replies
3.3k
views
Cannot download “EBImage” library in R
R EBImage
written 5.3 years ago by • 0
0
votes
0
replies
1.5k
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
5.4 years ago mmartin ▴ 20
0
votes
1
reply
1.5k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
2
votes
4
replies
1.8k
views
Bioconductor package development
package R software development
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
1
vote
6
replies
2.3k
views
How to create geneselectionfunction in TopGO: Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector
R TopGO Geneenrichment
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
votes
2
replies
1.8k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
5.4 years ago Marco_aurelio • 0
0
votes
0
replies
911
views
plots in gwasurvivr
gwasurvivr r survival cox
5.4 years ago laura.martinez.campelo • 0
0
votes
2
replies
2.7k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
3
votes
16
replies
6.6k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 4.3 years ago by ▴ 10 • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.9k
views
K Means Clustering Two Matrices for ComplexHeatmap
complexheatmap R
5.5 years ago pthom010 • 0
2
votes
6
replies
4.7k
views
Can't install package oligoClasses
R oligoClasses ff
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 20
3
votes
1
reply
1.2k
views
Create a '.db' package for agilent
R agilent microarray
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 20
0
votes
2
replies
1.2k
views
How to normalise data in ballgown?
r normalization edger
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
5
votes
8
replies
2.5k
views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
updated 5.5 years ago by ▴ 220 • written 5.5 years ago by ▴ 10
1
vote
4
replies
2.7k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Differential gene expression using Ballgown
r normalization
5.5 years ago lakshmi9c • 0
0
votes
4
replies
3.4k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by • 0
0
votes
1
reply
1.1k
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 5.5 years ago by ★ 4.0k • written 5.5 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 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
0
votes
3
replies
2.1k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.5 years ago TriS ▴ 200
0
votes
2
replies
1.9k
views
Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 5.5 years ago by ★ 4.0k • written 5.6 years ago by ▴ 40
0
votes
3
replies
1.6k
views
Use topGOdata in devtools package
topGO devtools R
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
2
votes
1
reply
3.6k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 60
2
votes
4
replies
13k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 60
6
votes
11
replies
3.0k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 5.6 years ago by ★ 6.6k • written 5.6 years ago by • 0
2
votes
3
replies
1.3k
views
Annotation of Genomic Regions
annotation genomic regions R
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
4
replies
1.6k
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
5.6 years ago Arpi Beshlikyan • 0
2
votes
1
reply
845
views
diffbind from own binding affinity table
diffbind R
updated 5.6 years ago by ★ 5.3k • written 5.6 years ago by • 0
0
votes
7
replies
2.2k
views
WGCNA to Cytoscape error
R
5.6 years ago zen • 0
0
votes
6
replies
2.2k
views
Error when trying to access BiomaRt from a cluster
biomaRt R cluster
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
0
votes
1
reply
1.0k
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
5.6 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 4.0 years ago by • 0 • written 5.6 years ago by • 0
0
votes
5
replies
2.0k
views
DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 5.6 years ago by ★ 4.0k • written 5.6 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 5.2 years ago by ▴ 30 • written 5.6 years ago by • 0
3
votes
3
replies
1.9k
views
How can I use 'geom_taxalink()' with the circular layout in the 'ggtree' package in R?
r ggtree phylogeny
updated 5.6 years ago by ★ 1.2k • written 5.6 years ago by ▴ 10
1
vote
3
replies
3.7k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 3.0 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
votes
0
replies
2.4k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
genomics NGS R genetics statistics
7.6 years ago • updated 5.3 years ago Luo Weijun ★ 1.6k
0
votes
8
replies
1.4k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
updated 5.7 years ago by 43k • written 5.7 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 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
12
replies
2.1k
views
Taking much longer time for same script after R upgrade to 4.0
R
5.7 years ago hsiowa2 ▴ 20
3
votes
5
replies
1.3k
views
How to loop over two files ...and calculate R^2 between SNPs
loops R
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 10
0
votes
9
replies
2.6k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.7 years ago camillab. ▴ 10
1
vote
0
replies
1.7k
views
Job: Bioinformatics Data Analyst
R RNA-seq job Job
5.7 years ago António Miguel de Jesus Domingues ▴ 510
1
vote
3
replies
1.0k
views
Use Tx2Gene for Annotation
deseq2 annotation r
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1,163 results • Page 5 of 24
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Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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