Showing : RSTUDIO • reset
0
votes
7
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2.4k
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
votes
0
replies
550
views
RN to EC Mapping Not Working for Some Nodes
RStudio ggkegg
updated 17 months ago by 68k • written 17 months ago by • 0
2
votes
3
replies
933
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
17 months ago R_Page • 0
0
votes
2
replies
1.1k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
18 months ago • updated 17 months ago yee • 0
1
vote
3
replies
932
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 18 months ago by 68k • written 18 months ago by • 0
4
votes
6
replies
2.9k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 7 months ago by • 0 • written 18 months ago by • 0
0
votes
7
replies
3.9k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
1
reply
704
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
0
votes
1
reply
2.6k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
0
votes
2
replies
1.6k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 2.4 years ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
1.3k
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio MOFA2 bug knitr
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 430
0
votes
1
reply
1.2k
views
Issue with installation of a package.
RStudio flowFDA
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
votes
14
replies
5.7k
views
GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 2.6 years ago by • 0 • written 2.9 years ago by • 0
4
votes
5
replies
3.2k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 3.1 years ago by • 0
0
votes
0
replies
1.7k
views
function GDCquery_Maf error
rstudio maftools
3.1 years ago misslubblys • 0
9
votes
14
replies
9.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 10 months ago by 4.1k • written 3.3 years ago by ▴ 40
0
votes
3
replies
2.0k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.2 years ago by 21k • written 3.3 years ago by ▴ 10
0
votes
0
replies
861
views
Read the first sequence from fasta file - TFBSTool
TFBSTools FASTA RStudio
3.5 years ago HELEN • 0
0
votes
1
reply
1.2k
views
TFBSTools and readFASTA
TFBSTools DNASeqData readFASTA DNA RStudio
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
0
replies
866
views
TFBSTools- analysis for trascriprion factors
TFBSTools RStudio R
3.6 years ago HELEN • 0
1
vote
5
replies
3.2k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
3.6 years ago Sonia • 0
0
votes
1
reply
2.9k
views
Unable to Install packages in R
rstudio
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
4
replies
4.2k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.7 years ago HELEN • 0
5
votes
15
replies
17k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
1
vote
7
replies
4.4k
views
Error with hclust
dendrogram hclust textanalysis R RStudio
4.1 years ago Abby ▴ 10
0
votes
1
reply
1.2k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 4.2 years ago by ▴ 150 • written 4.3 years ago by • 0
1
vote
5
replies
6.1k
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 4.5 years ago by ★ 11k • written 4.5 years ago by • 0
0
votes
1
reply
1.2k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.2 years ago by 4.1k • written 5.2 years ago by • 0
0
votes
5
replies
2.2k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 5.5 years ago by ▴ 20 • written 5.5 years ago by • 0
2
votes
1
reply
11k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 20
0
votes
5
replies
2.3k
views
Using RStudio AMI with localhost
RStudio AWS AMI
5.9 years ago bio-explorer • 0
3
votes
6
replies
2.2k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 30
1
vote
8
replies
3.2k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
0
votes
0
replies
2.2k
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
6.1 years ago fatimarasool135 • 0
2
votes
4
replies
2.3k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 2.1 years ago by ▴ 10 • written 6.5 years ago by • 0
0
votes
4
replies
2.0k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
votes
2
replies
4.5k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
0
votes
1
reply
1.8k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 20
0
votes
1
reply
2.2k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 6.9 years ago by 43k • written 6.9 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
7.0 years ago arphatak • 0
1
vote
4
replies
2.0k
views
biomaRt scan error for latest assembly when indicating version Number
biomart rstudio ensembl mart
updated 7.2 years ago by ★ 6.6k • written 7.2 years ago by • 0
2
votes
4
replies
1.6k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 10
0
votes
2
replies
4.3k
views
Error in file.choose() : file choice cancelled
package development bioconductor rstudio rmarkdown vignettes
7.5 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
7.5 years ago biostR ▴ 10
0
votes
0
replies
2.0k
views
Problem with heatmap by ComplexHeatmap
complexheatmap Rstudio NOISeq
7.7 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 7.8 years ago by 25k • written 7.8 years ago by • 0
1
vote
1
reply
5.4k
views
MA plot in R
rstudio r plotMA
7.9 years ago g.k • 0
0
votes
3
replies
3.0k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
7.9 years ago mszskb • 0
0
votes
4
replies
1.8k
views
problem in installing flowclust
rstudio flowclust
updated 8.0 years ago by 4.1k • written 8.0 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 8.0 years ago by ▴ 360 • written 8.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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