Showing : Rstudio • reset
0
votes
7
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2.6k
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
0
votes
0
replies
630
views
RN to EC Mapping Not Working for Some Nodes
RStudio ggkegg
updated 22 months ago by 68k • written 22 months ago by • 0
2
votes
3
replies
1.1k
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
23 months ago R_Page • 0
0
votes
2
replies
1.2k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
23 months ago yee • 0
1
vote
3
replies
1.1k
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 23 months ago by 68k • written 23 months ago by • 0
4
votes
6
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3.4k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 12 months ago by • 0 • written 24 months ago by • 0
0
votes
7
replies
4.2k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 23 months ago by 68k • written 24 months ago by • 0
0
votes
1
reply
828
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
1
reply
2.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
2
replies
1.8k
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 2.8 years ago by • 0 • written 3.0 years ago by • 0
0
votes
1
reply
1.4k
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio MOFA2 bug knitr
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 430
0
votes
1
reply
1.4k
views
Issue with installation of a package.
RStudio flowFDA
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
votes
14
replies
6.1k
views
GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 3.1 years ago by • 0 • written 3.3 years ago by • 0
4
votes
5
replies
3.3k
views
DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 3.5 years ago by • 0
0
votes
0
replies
1.8k
views
function GDCquery_Maf error
rstudio maftools
3.5 years ago misslubblys • 0
9
votes
14
replies
9.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 15 months ago by 4.2k • written 3.8 years ago by ▴ 40
0
votes
3
replies
2.1k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.7 years ago by 21k • written 3.8 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Read the first sequence from fasta file - TFBSTool
TFBSTools FASTA RStudio
4.0 years ago HELEN • 0
0
votes
1
reply
1.3k
views
TFBSTools and readFASTA
TFBSTools DNASeqData readFASTA DNA RStudio
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
0
replies
939
views
TFBSTools- analysis for trascriprion factors
TFBSTools RStudio R
4.0 years ago HELEN • 0
1
vote
5
replies
3.4k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
4.1 years ago Sonia • 0
0
votes
1
reply
3.0k
views
Unable to Install packages in R
rstudio
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
votes
4
replies
4.5k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq rstudio fasta Biostrings csv
4.2 years ago HELEN • 0
5
votes
15
replies
18k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
1
vote
7
replies
4.7k
views
Error with hclust
dendrogram hclust textanalysis R RStudio
4.6 years ago • updated 4.5 years ago Abby ▴ 10
0
votes
1
reply
1.3k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 4.7 years ago by ▴ 150 • written 4.7 years ago by • 0
1
vote
5
replies
6.3k
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 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
0
votes
1
reply
1.3k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
votes
5
replies
2.4k
views
readTranscriptFeatures from genomation
R Rstudio Error readTranscriptFeatures genomation
updated 5.9 years ago by ▴ 20 • written 5.9 years ago by • 0
2
votes
1
reply
11k
views
Error: status was 'SSL connect error'
bioconductor proxy macOS R RStudio
updated 6.0 years ago by 25k • written 6.0 years ago by ▴ 20
0
votes
5
replies
2.4k
views
Using RStudio AMI with localhost
RStudio AWS AMI
6.3 years ago bio-explorer • 0
3
votes
6
replies
2.4k
views
Integer overflow issue with ChIPQC
ChIPQC Rstudio
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 30
1
vote
8
replies
3.4k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2 null summarizedexperiment rstudio
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
0
votes
0
replies
2.3k
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
6.5 years ago fatimarasool135 • 0
2
votes
4
replies
2.5k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 2.5 years ago by ▴ 10 • written 6.9 years ago by • 0
0
votes
4
replies
2.1k
views
New computer won't install DESeq2
deseq2 rstudio install error
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
2
replies
4.6k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
1
reply
1.9k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 20
0
votes
1
reply
2.3k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
0
replies
1.4k
views
Running ASpli on R results in "Error: vector memory exhausted (limit reached?)"
aspli rstudio
7.4 years ago arphatak • 0
1
vote
4
replies
2.1k
views
biomaRt scan error for latest assembly when indicating version Number
biomart rstudio ensembl mart
updated 7.7 years ago by ★ 6.6k • written 7.7 years ago by • 0
2
votes
4
replies
1.7k
views
R session terminates when trying to load affycoretools package
affycoretools Rstudio fatal error
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 10
0
votes
2
replies
4.4k
views
Error in file.choose() : file choice cancelled
package development bioconductor rstudio rmarkdown vignettes
7.9 years ago clarisbaby • 0
1
vote
2
replies
1.7k
views
Rstudio session aborts when using read.celfiles()
oligo package Rstudio fatal error microarray CEL
7.9 years ago biostR ▴ 10
0
votes
0
replies
2.1k
views
Problem with heatmap by ComplexHeatmap
complexheatmap Rstudio NOISeq
8.1 years ago Luiz • 0
0
votes
1
reply
2.3k
views
Trouble installing Bioconductor in R-studio (R version 3.3.1)
bioconductor rstudio
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
1
vote
1
reply
5.5k
views
MA plot in R
rstudio r plotMA
8.4 years ago g.k • 0
0
votes
3
replies
3.2k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio cummerbund error
8.4 years ago mszskb • 0
0
votes
4
replies
1.9k
views
problem in installing flowclust
rstudio flowclust
updated 8.4 years ago by 4.2k • written 8.4 years ago by • 0
0
votes
1
reply
1.5k
views
can a function outliers be applied for a flowframe?
bioconductor flow cytometry rstudio
updated 8.4 years ago by ▴ 360 • written 8.4 years ago by • 0
77 results • Page 1 of 2
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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