Showing : RSTUDIO • reset
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 6 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
5
votes
15
replies
11k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
4
votes
5
replies
2.1k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 24 months ago by • 0
3
votes
8
replies
26k
views
"Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
BiocUpgrade Rstudio Bioconductor R3.2.2
8.5 years ago svlachavas ▴ 830
3
votes
3
replies
16k
views
Error in Knit R Markdown document (could not find function "Biocexptpkg")
rmarkdown rstudio knitr
7.5 years ago Jon Bråte ▴ 250
3
votes
6
replies
1.8k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 4.8 years ago by 25k • written 4.8 years ago by ▴ 30
3
votes
7
replies
4.5k
views
goseq code after DESeq2 -NO IDEA!
goseq DESEQ2 RSTUDIO CODE
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
2
votes
3
replies
483
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
4 months ago R_Page • 0
2
votes
1
reply
8.3k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 20
2
votes
4
replies
1.7k
views
RStudio quits unexpectedly while running DiffBind on R 3.4.0
software error diffbind rstudio abort quit
updated 7.0 years ago by ▴ 650 • written 7.0 years ago by • 0
2
votes
4
replies
1.7k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 12 months ago by • 0 • written 5.4 years ago by • 0
2
votes
1
reply
4.5k
views
Reading fasta file with multiple sequences
multiple sequences bioconductor rstudio seqinr
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
2
votes
5
replies
5.4k
views
Update R in Rstudio to specific version 3.2.1 in windows
updateR rstudio Rversion3.2.1
updated 8.6 years ago by ★ 8.2k • written 8.6 years ago by ▴ 830
2
votes
2
replies
3.8k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
2
votes
4
replies
1.3k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 10
2
votes
18
replies
3.1k
views
edgeR: processAmplicons crashes with large number of hairpins
edger processamplicons rstudio
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
2
votes
5
replies
759
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
5 months ago j_denton • 0
1
vote
5
replies
2.2k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
2.6 years ago Sonia • 0
1
vote
8
replies
2.7k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
1
vote
3
replies
3.5k
views
Problem using display() function on RStudio
display rstudio annotationhub
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 10
1
vote
3
replies
23k
views
Converting first column to rownames
rstudio
8.2 years ago John ▴ 30
1
vote
1
reply
4.9k
views
MA plot in R
rstudio r plotMA
6.9 years ago g.k • 0
1
vote
2
replies
1.3k
views
Rstudio session aborts when using read.celfiles()
oligo package Rstudio fatal error microarray CEL
6.4 years ago biostR ▴ 10
1
vote
4
replies
1.6k
views
biomaRt scan error for latest assembly when indicating version Number
biomart rstudio ensembl mart
updated 6.2 years ago by ★ 6.5k • written 6.2 years ago by • 0
1
vote
5
replies
4.0k
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 3.4 years ago by ★ 11k • written 3.4 years ago by • 0
1
vote
7
replies
2.8k
views
Error with hclust
dendrogram hclust textanalysis R RStudio
3.1 years ago • updated 3.0 years ago Abby ▴ 10
1
vote
3
replies
448
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
2
replies
1.1k
views
Problem with cummeRbund
rstudio cummerbund
7.1 years ago sanathoi.guru • 0
0
votes
0
replies
1.1k
views
Rstudio crashes when running monocole
monocole single-cell rstudio
7.0 years ago Assa Yeroslaviz ★ 1.5k
0
votes
4
replies
3.1k
views
Impossible to use goseq package - problem with geneLenDataBase
goseq geneLenDataBase bioclite rstudio
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
can a function outliers be applied for a flowframe?
bioconductor flow cytometry rstudio
updated 6.9 years ago by ▴ 350 • written 6.9 years ago by • 0
0
votes
4
replies
1.4k
views
problem in installing flowclust
rstudio flowclust
updated 6.9 years ago by 3.8k • written 6.9 years ago by • 0
0
votes
3
replies
2.6k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
6.9 years ago mszskb • 0
0
votes
4
replies
1.6k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
1
reply
1.9k
views
Trouble installing Bioconductor in R-studio (R version 3.3.1)
bioconductor rstudio
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
0
replies
1.5k
views
Problem with heatmap by ComplexHeatmap
complexheatmap Rstudio NOISeq
6.6 years ago Luiz • 0
0
votes
8
replies
224
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 hours ago by ★ 1.3k • written 2 days ago by • 0
0
votes
2
replies
3.6k
views
Error in file.choose() : file choice cancelled
package development bioconductor rstudio rmarkdown vignettes
6.4 years ago clarisbaby • 0
0
votes
1
reply
379
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
votes
3
replies
1.3k
views
GenomiFeatures is not available for R version 3.2.1
GenomiFeatures rversion3.2.1 3.0 rstudio
8.6 years ago serpalma.v ▴ 60
0
votes
0
replies
1.0k
views
Running ASpli on R results in "Error: vector memory exhausted (limit reached?)"
aspli rstudio
5.9 years ago arphatak • 0
0
votes
1
reply
1.2k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
8.6 years ago svlachavas ▴ 830
0
votes
9
replies
2.4k
views
is AClust package still available?
Aclust Aclustering Rstudio Clusters
updated 8.7 years ago by ▴ 40 • written 8.7 years ago by ▴ 10
0
votes
0
replies
1.7k
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
5.0 years ago fatimarasool135 • 0
0
votes
3
replies
2.1k
views
Getting different results with DESeq2
deseq2 results rstudio
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 10
0
votes
5
replies
1.6k
views
Using RStudio AMI with localhost
RStudio AWS AMI
4.8 years ago bio-explorer • 0
0
votes
20
replies
6.1k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
0
votes
5
replies
1.5k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 4.4 years ago by ▴ 20 • written 4.4 years ago by • 0
0
votes
1
reply
923
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.2 years ago by 3.8k • written 4.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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