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Rstudio
•
reset
0
votes
7
replies
1.3k
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 months ago by
swbarnes2
★ 1.4k • written 7 months ago by
Aaliya
• 0
0
votes
0
replies
443
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 11 months ago by
James W. MacDonald
67k • written 11 months ago by
Ramirj49
• 0
2
votes
3
replies
750
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
810
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
12 months ago
yee
• 0
1
vote
3
replies
723
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 12 months ago by
James W. MacDonald
67k • written 13 months ago by
j_denton
• 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 9 weeks ago by
MauriAndres
• 0 • written 13 months ago by
j_denton
• 0
0
votes
7
replies
2.8k
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
James W. MacDonald
67k • written 13 months ago by
BioES
• 0
0
votes
1
reply
595
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 16 months ago by
ATpoint
★ 4.6k • written 16 months ago by
DrFizz
• 0
0
votes
1
reply
1.7k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 16 months ago by
ATpoint
★ 4.6k • written 16 months ago by
DrFizz
• 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
Christian Mertes
• 0 • written 2.1 years ago by
me.achleitner
• 0
0
votes
1
reply
1.1k
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio
MOFA2
bug
knitr
updated 2.1 years ago by
James W. MacDonald
67k • written 2.1 years ago by
Kevin Coombes
▴ 430
0
votes
1
reply
1.0k
views
Issue with installation of a package.
RStudio
flowFDA
updated 2.2 years ago by
Basti
▴ 780 • written 2.2 years ago by
kinoshamoodley
• 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
wshao9
• 0 • written 2.4 years ago by
JoseR
• 0
4
votes
5
replies
2.8k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 2.6 years ago by
960942
• 0
0
votes
0
replies
1.5k
views
function GDCquery_Maf error
rstudio
maftools
2.7 years ago
misslubblys
• 0
9
votes
14
replies
7.6k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 4 months ago by
shepherl
4.1k • written 2.9 years ago by
jon.klonowski
▴ 40
0
votes
3
replies
1.8k
views
Reading large file (15GB) in R
R
Rstudio
Bioconducter
statistics
updated 2.8 years ago by
Sean Davis
21k • written 2.9 years ago by
Jitendra
▴ 10
0
votes
0
replies
768
views
Read the first sequence from fasta file - TFBSTool
TFBSTools
FASTA
RStudio
3.1 years ago
HELEN
• 0
0
votes
1
reply
979
views
TFBSTools and readFASTA
TFBSTools
DNASeqData
readFASTA
DNA
RStudio
updated 3.1 years ago by
James W. MacDonald
67k • written 3.1 years ago by
HELEN
• 0
0
votes
0
replies
760
views
TFBSTools- analysis for trascriprion factors
TFBSTools
RStudio
R
3.1 years ago
HELEN
• 0
1
vote
5
replies
2.7k
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 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
Fiona
• 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 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
KOUSTAV
• 0
1
vote
7
replies
3.7k
views
Error with hclust
dendrogram
hclust
textanalysis
R
RStudio
3.7 years ago • updated 3.6 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
Erik Wright
▴ 150 • written 3.8 years ago by
noeliaruizalonso23
• 0
1
vote
5
replies
5.1k
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 4.0 years ago by
Michael Lawrence
★ 11k • written 4.0 years ago by
Søren
• 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
shepherl
4.1k • written 4.8 years ago by
bwiley4
• 0
0
votes
5
replies
1.9k
views
readTranscriptFeatures from genomation
R
Rstudio
Error
readTranscriptFeatures
genomation
updated 5.0 years ago by
altuna akalin
▴ 20 • written 5.0 years ago by
hwaterma
• 0
2
votes
1
reply
9.7k
views
Error: status was 'SSL connect error'
bioconductor
proxy
macOS
R
RStudio
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
mcall
▴ 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
Martin Morgan
25k • written 5.4 years ago by
Nitesh Kumar Singh
▴ 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
Martin Morgan
25k • written 5.5 years ago by
200dumplings
• 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
2.0k
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
updated 19 months ago by
Shreyash
▴ 10 • written 6.0 years ago by
rtwest
• 0
0
votes
4
replies
1.9k
views
New computer won't install DESeq2
deseq2
rstudio
install error
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
jyoung
• 0
2
votes
2
replies
4.2k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio
heatmap.2
updated 6.3 years ago by
James W. MacDonald
67k • written 6.3 years ago by
austin.taylor
• 0
0
votes
1
reply
1.5k
views
Install Bioconductor package locally/temporarily
R
rstudio
package installation
updated 6.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
ariel
▴ 20
0
votes
1
reply
2.1k
views
DeSeq2 installation on ubuntu fails
deseq2
R
ubuntu
bioconductor
rstudio
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
drumarsohail
• 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
Mike Smith
★ 6.6k • written 6.8 years ago by
mullpaul
• 0
2
votes
4
replies
1.4k
views
R session terminates when trying to load affycoretools package
affycoretools
Rstudio
fatal error
updated 6.8 years ago by
James W. MacDonald
67k • written 6.8 years ago by
biostR
▴ 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
7.2 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
Martin Morgan
25k • written 7.4 years ago by
yog312
• 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
1.6k
views
problem in installing flowclust
rstudio
flowclust
updated 7.5 years ago by
shepherl
4.1k • written 7.5 years ago by
shadhiksk
• 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
SamGG
▴ 360 • written 7.5 years ago by
shadhiksk
• 0
50 results • Page
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Answer: sva: get a sv for RIN scores
by
Gordon Smyth
52k
Surrogate variables are not constructed from known variates, so one doesn't get surrogate variables for RIN scores. I am guessing that the …
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
by
alexandra.casey
• 0
any update? It's still not working for me. I'm amazed it's taking this long to fix!
Comment: git push errors
by
Jiping Wang
▴ 90
I have bioconductor remote named "upstream". thanks for help!! I missed ":devel" after master. ``` (base) jon@Jipings-2021-macbook-pro Rib…
Answer: git push errors
by
James W. MacDonald
67k
This is a question for the bioc-devel listserv (bioc-devel@r-project.org) rather than the support site. However, it looks like you are s…
Comment: How to annotate a limma Elist raw class object with an annotation file
by
James W. MacDonald
67k
Oh right. My bad. Good for you though, figuring out that it's ENTREZID, not ENTREZGENE. You did a good job of reading the error message in …
Votes
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
A: DESeq2 One-way ANOVA with 3 sample groups?
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