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0
votes
2
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11k
views
Add selected row names on pheatmap
R pheatmap
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by ▴ 30
7
votes
6
replies
5.0k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
4.9 years ago ecg1g15 ▴ 30
9
votes
5
replies
5.2k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
4.9 years ago ecg1g15 ▴ 30
0
votes
0
replies
1.2k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
4.9 years ago • updated 4.6 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 4.9 years ago by 4.2k • written 4.9 years ago by • 0
0
votes
3
replies
3.9k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode : logical
R DESeq2
4.9 years ago Ricard Lambea • 0
2
votes
6
replies
3.1k
views
Cannot download “EBImage” library in R
R EBImage
written 4.9 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
5.0 years ago mmartin ▴ 20
0
votes
1
reply
1.3k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
votes
4
replies
1.6k
views
Bioconductor package development
package R software development
updated 5.0 years ago by 25k • written 5.0 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 5.0 years ago by 68k • written 5.1 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
5.1 years ago Marco_aurelio • 0
0
votes
0
replies
820
views
plots in gwasurvivr
gwasurvivr r survival cox
5.1 years ago laura.martinez.campelo • 0
0
votes
2
replies
2.4k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
3
votes
16
replies
6.2k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 4.0 years ago by ▴ 10 • written 5.1 years ago by ▴ 10
0
votes
2
replies
1.7k
views
K Means Clustering Two Matrices for ComplexHeatmap
complexheatmap R
5.1 years ago pthom010 • 0
2
votes
6
replies
4.5k
views
Can't install package oligoClasses
R oligoClasses ff
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 20
3
votes
1
reply
1.1k
views
Create a '.db' package for agilent
R agilent microarray
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 20
0
votes
2
replies
1.0k
views
How to normalise data in ballgown?
r normalization edger
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
5
votes
8
replies
2.2k
views
Sort decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort R RNAseq character numeric
updated 5.1 years ago by ▴ 220 • written 5.1 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 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Differential gene expression using Ballgown
r normalization
5.1 years ago lakshmi9c • 0
0
votes
4
replies
2.8k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.1 years ago by ★ 1.3k • written 5.1 years ago by • 0
0
votes
1
reply
1.1k
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 20
2
votes
5
replies
1.5k
views
the results from normalized=TRUE and normalized = FALSE is the same
R deseq2
updated 5.1 years ago by 43k • written 5.2 years ago by ▴ 20
0
votes
3
replies
2.0k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.2 years ago TriS ▴ 200
0
votes
2
replies
1.8k
views
Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 40
0
votes
3
replies
1.4k
views
Use topGOdata in devtools package
topGO devtools R
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
votes
1
reply
3.2k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 60
2
votes
4
replies
12k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 5.2 years ago by ★ 4.0k • written 5.2 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 5.2 years ago by ★ 6.6k • written 5.2 years ago by • 0
2
votes
3
replies
1.2k
views
Annotation of Genomic Regions
annotation genomic regions R
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
vote
4
replies
1.4k
views
Subsampling when adjusting the read start sites in the ATACseqQC guide
atacseqqc r
5.2 years ago Arpi Beshlikyan • 0
2
votes
1
reply
789
views
diffbind from own binding affinity table
diffbind R
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by • 0
0
votes
7
replies
2.0k
views
WGCNA to Cytoscape error
R
5.2 years ago zen • 0
0
votes
6
replies
2.0k
views
Error when trying to access BiomaRt from a cluster
biomaRt R cluster
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
0
votes
1
reply
948
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
5.2 years ago Ankit ▴ 20
0
votes
2
replies
1.5k
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 3.6 years ago by • 0 • written 5.2 years ago by • 0
0
votes
5
replies
1.6k
views
DRIMSeq with technical replicates
DRIMSeq R DTU technical replicates deseq2
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
0
votes
1
reply
1.1k
views
Importing Newick trees in Cytoscape by conversion to igraph via RCy3
RCy3 Cytoscape R Newick Bioconductor
updated 4.8 years ago by ▴ 30 • written 5.2 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 5.2 years ago by ★ 1.2k • written 5.3 years ago by ▴ 10
1
vote
3
replies
3.5k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 2.6 years ago by ★ 4.0k • written 5.3 years ago by • 0
0
votes
0
replies
2.3k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
genomics NGS R genetics statistics
7.3 years ago • updated 4.9 years ago Luo Weijun ★ 1.6k
0
votes
8
replies
1.2k
views
Deseq2 weird values for Log2FC and pvalue.
deseq2 rnaseq r
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
2
replies
1.8k
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 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
12
replies
1.9k
views
Taking much longer time for same script after R upgrade to 4.0
R
5.3 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 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
0
votes
9
replies
2.4k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.3 years ago camillab. ▴ 10
1
vote
0
replies
1.5k
views
Job: Bioinformatics Data Analyst
R RNA-seq job Job
5.3 years ago António Miguel de Jesus Domingues ▴ 510
1
vote
3
replies
900
views
Use Tx2Gene for Annotation
deseq2 annotation r
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1,163 results • Page 5 of 24
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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