Showing : RStudio • reset
0
votes
7
replies
1.4k
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
0
replies
447
views
RN to EC Mapping Not Working for Some Nodes
RStudio ggkegg
updated 12 months ago by 67k • written 12 months ago by • 0
2
votes
3
replies
769
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
12 months ago R_Page • 0
0
votes
2
replies
836
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
13 months ago • updated 12 months ago yee • 0
1
vote
3
replies
741
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 13 months ago by 67k • written 13 months ago by • 0
4
votes
6
replies
1.8k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 11 weeks ago by • 0 • written 13 months ago by • 0
0
votes
7
replies
2.9k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
0
votes
1
reply
598
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
0
votes
1
reply
1.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 16 months ago by ★ 4.6k • written 16 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 23 months ago by • 0 • written 2.1 years ago by • 0
0
votes
1
reply
1.1k
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio MOFA2 bug knitr
updated 2.2 years ago by 67k • written 2.2 years ago by ▴ 430
0
votes
1
reply
1.0k
views
Issue with installation of a package.
RStudio flowFDA
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
0
votes
14
replies
5.0k
views
GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 2.2 years ago by • 0 • written 2.5 years ago by • 0
4
votes
5
replies
2.8k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 2.7 years ago by • 0
0
votes
0
replies
1.5k
views
function GDCquery_Maf error
rstudio maftools
2.7 years ago misslubblys • 0
9
votes
14
replies
7.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 5 months ago by 4.1k • written 2.9 years ago by ▴ 40
0
votes
3
replies
1.8k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 2.8 years ago by 21k • written 2.9 years ago by ▴ 10
0
votes
0
replies
775
views
Read the first sequence from fasta file - TFBSTool
TFBSTools FASTA RStudio
3.1 years ago HELEN • 0
0
votes
1
reply
988
views
TFBSTools and readFASTA
TFBSTools DNASeqData readFASTA DNA RStudio
updated 3.1 years ago by 67k • written 3.1 years ago by • 0
0
votes
0
replies
767
views
TFBSTools- analysis for trascriprion factors
TFBSTools RStudio R
3.2 years ago HELEN • 0
1
vote
5
replies
2.8k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
3.2 years ago Sonia • 0
0
votes
1
reply
2.5k
views
Unable to Install packages in R
rstudio
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
0
votes
4
replies
3.7k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
3.3 years ago HELEN • 0
5
votes
15
replies
14k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
1
vote
7
replies
3.7k
views
Error with hclust
dendrogram hclust textanalysis R RStudio
3.7 years ago Abby ▴ 10
0
votes
1
reply
1.0k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 3.8 years ago by ▴ 150 • written 3.8 years ago by • 0
1
vote
5
replies
5.2k
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 4.1 years ago by ★ 11k • written 4.1 years ago by • 0
0
votes
1
reply
1.1k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.8 years ago by 4.1k • written 4.8 years ago by • 0
0
votes
5
replies
2.0k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 5.1 years ago by ▴ 20 • written 5.1 years ago by • 0
2
votes
1
reply
9.8k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 20
0
votes
5
replies
2.0k
views
Using RStudio AMI with localhost
RStudio AWS AMI
5.4 years ago bio-explorer • 0
3
votes
6
replies
2.1k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 30
1
vote
8
replies
3.0k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
0
votes
0
replies
2.0k
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
5.7 years ago fatimarasool135 • 0
2
votes
4
replies
2.1k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 20 months ago by ▴ 10 • written 6.0 years ago by • 0
0
votes
4
replies
1.9k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
2
replies
4.3k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
0
votes
1
reply
1.5k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 20
0
votes
1
reply
2.1k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
0
replies
1.2k
views
Running ASpli on R results in "Error: vector memory exhausted (limit reached?)"
aspli rstudio
6.5 years ago arphatak • 0
1
vote
4
replies
1.8k
views
biomaRt scan error for latest assembly when indicating version Number
biomart rstudio ensembl mart
updated 6.8 years ago by ★ 6.6k • written 6.8 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 6.8 years ago by 67k • written 6.8 years ago by ▴ 10
0
votes
2
replies
4.0k
views
Error in file.choose() : file choice cancelled
package development bioconductor rstudio rmarkdown vignettes
7.1 years ago clarisbaby • 0
1
vote
2
replies
1.5k
views
Rstudio session aborts when using read.celfiles()
oligo package Rstudio fatal error microarray CEL
7.1 years ago biostR ▴ 10
0
votes
0
replies
1.8k
views
Problem with heatmap by ComplexHeatmap
complexheatmap Rstudio NOISeq
7.3 years ago Luiz • 0
0
votes
1
reply
2.1k
views
Trouble installing Bioconductor in R-studio (R version 3.3.1)
bioconductor rstudio
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
1
vote
1
reply
5.2k
views
MA plot in R
rstudio r plotMA
7.5 years ago g.k • 0
0
votes
3
replies
2.9k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
7.5 years ago mszskb • 0
0
votes
4
replies
1.7k
views
problem in installing flowclust
rstudio flowclust
updated 7.5 years ago by 4.1k • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
can a function outliers be applied for a flowframe?
bioconductor flow cytometry rstudio
updated 7.5 years ago by ▴ 360 • written 7.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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