Showing : Rstudio • reset
0
votes
7
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1.9k
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
0
votes
0
replies
500
views
RN to EC Mapping Not Working for Some Nodes
RStudio ggkegg
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
3
replies
833
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
15 months ago R_Page • 0
0
votes
2
replies
947
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
15 months ago yee • 0
1
vote
3
replies
819
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 15 months ago by 68k • written 16 months ago by • 0
4
votes
6
replies
2.3k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 5 months ago by • 0 • written 16 months ago by • 0
0
votes
7
replies
3.4k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
1
reply
651
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
0
votes
1
reply
2.1k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
0
votes
2
replies
1.5k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 2.2 years ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
1.2k
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio MOFA2 bug knitr
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 430
0
votes
1
reply
1.1k
views
Issue with installation of a package.
RStudio flowFDA
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
votes
14
replies
5.3k
views
GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 2.4 years ago by • 0 • written 2.7 years ago by • 0
4
votes
5
replies
3.0k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.8 years ago by • 0
0
votes
0
replies
1.6k
views
function GDCquery_Maf error
rstudio maftools
2.9 years ago misslubblys • 0
9
votes
14
replies
8.3k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 7 months ago by 4.1k • written 3.1 years ago by ▴ 40
0
votes
3
replies
1.9k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.0 years ago by 21k • written 3.1 years ago by ▴ 10
0
votes
0
replies
817
views
Read the first sequence from fasta file - TFBSTool
TFBSTools FASTA RStudio
3.3 years ago HELEN • 0
0
votes
1
reply
1.1k
views
TFBSTools and readFASTA
TFBSTools DNASeqData readFASTA DNA RStudio
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
0
replies
816
views
TFBSTools- analysis for trascriprion factors
TFBSTools RStudio R
3.4 years ago HELEN • 0
1
vote
5
replies
2.9k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
3.4 years ago Sonia • 0
0
votes
1
reply
2.7k
views
Unable to Install packages in R
rstudio
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
4
replies
4.0k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.5 years ago HELEN • 0
5
votes
15
replies
15k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
1
vote
7
replies
4.1k
views
Error with hclust
dendrogram hclust textanalysis R RStudio
3.9 years ago Abby ▴ 10
0
votes
1
reply
1.1k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 4.0 years ago by ▴ 150 • written 4.0 years ago by • 0
1
vote
5
replies
5.6k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw rtracklayer http RStudio
updated 4.3 years ago by ★ 11k • written 4.3 years ago by • 0
0
votes
1
reply
1.2k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.0 years ago by 4.1k • written 5.0 years ago by • 0
0
votes
5
replies
2.1k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 5.3 years ago by ▴ 20 • written 5.3 years ago by • 0
2
votes
1
reply
10k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 20
0
votes
5
replies
2.1k
views
Using RStudio AMI with localhost
RStudio AWS AMI
5.6 years ago bio-explorer • 0
3
votes
6
replies
2.2k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 30
1
vote
8
replies
3.1k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
votes
0
replies
2.1k
views
Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels
software error ballgown rstudio R stattest
5.9 years ago fatimarasool135 • 0
2
votes
4
replies
2.2k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 22 months ago by ▴ 10 • written 6.2 years ago by • 0
0
votes
4
replies
1.9k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
votes
2
replies
4.4k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
1
reply
1.6k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 20
0
votes
1
reply
2.2k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
votes
0
replies
1.3k
views
Running ASpli on R results in "Error: vector memory exhausted (limit reached?)"
aspli rstudio
6.7 years ago arphatak • 0
1
vote
4
replies
1.9k
views
biomaRt scan error for latest assembly when indicating version Number
biomart rstudio ensembl mart
updated 7.0 years ago by ★ 6.6k • written 7.0 years ago by • 0
2
votes
4
replies
1.5k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 10
0
votes
2
replies
4.1k
views
Error in file.choose() : file choice cancelled
package development bioconductor rstudio rmarkdown vignettes
7.3 years ago clarisbaby • 0
1
vote
2
replies
1.6k
views
Rstudio session aborts when using read.celfiles()
oligo package Rstudio fatal error microarray CEL
7.3 years ago biostR ▴ 10
0
votes
0
replies
1.9k
views
Problem with heatmap by ComplexHeatmap
complexheatmap Rstudio NOISeq
7.5 years ago Luiz • 0
0
votes
1
reply
2.2k
views
Trouble installing Bioconductor in R-studio (R version 3.3.1)
bioconductor rstudio
updated 7.6 years ago by 25k • written 7.6 years ago by • 0
1
vote
1
reply
5.3k
views
MA plot in R
rstudio r plotMA
7.7 years ago g.k • 0
0
votes
3
replies
3.0k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
7.7 years ago mszskb • 0
0
votes
4
replies
1.7k
views
problem in installing flowclust
rstudio flowclust
updated 7.7 years ago by 4.1k • written 7.8 years ago by • 0
0
votes
1
reply
1.4k
views
can a function outliers be applied for a flowframe?
bioconductor flow cytometry rstudio
updated 7.7 years ago by ▴ 360 • written 7.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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