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RStudio
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0
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8
replies
338
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 9 days ago by
swbarnes2
★ 1.3k • written 10 days ago by
Aaliya
• 0
9
votes
11
replies
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 7 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
0
votes
0
replies
236
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
Ramirj49
• 0
2
votes
3
replies
500
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
5 months ago
R_Page
• 0
0
votes
2
replies
364
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
5 months ago
yee
• 0
1
vote
3
replies
465
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
j_denton
• 0
2
votes
5
replies
795
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio
convert
ensembldb
NCBI
6 months ago • updated 5 months ago
j_denton
• 0
0
votes
7
replies
1.6k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 6 months ago by
BioES
• 0
0
votes
1
reply
387
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
DrFizz
• 0
0
votes
1
reply
1.0k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
DrFizz
• 0
2
votes
4
replies
1.7k
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
updated 12 months ago by
Shreyash
▴ 10 • written 5.4 years ago by
rtwest
• 0
0
votes
2
replies
1.2k
views
Usinig BiocParallel package in R with M1 MAC
RStudio
R
M1
BiocParallel
Mac
updated 16 months ago by
Christian Mertes
• 0 • written 18 months ago by
me.achleitner
• 0
4
votes
5
replies
2.1k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 2.0 years ago by
960942
• 0
0
votes
1
reply
835
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio
MOFA2
bug
knitr
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Kevin Coombes
▴ 430
0
votes
1
reply
764
views
Issue with installation of a package.
RStudio
flowFDA
updated 19 months ago by
Basti
▴ 780 • written 19 months ago by
kinoshamoodley
• 0
0
votes
14
replies
4.1k
views
GenomeInfoDbData had non-zero exit status
DESeq2
RStudio
GenomeInfoDbData
hadnon-zeroexitstatus
updated 19 months ago by
wshao9
• 0 • written 22 months ago by
JoseR
• 0
0
votes
0
replies
1.2k
views
function GDCquery_Maf error
rstudio
maftools
2.1 years ago
misslubblys
• 0
0
votes
3
replies
1.5k
views
Reading large file (15GB) in R
R
Rstudio
Bioconducter
statistics
updated 2.2 years ago by
Sean Davis
21k • written 2.3 years ago by
Jitendra
▴ 10
0
votes
0
replies
640
views
Read the first sequence from fasta file - TFBSTool
TFBSTools
FASTA
RStudio
2.5 years ago
HELEN
• 0
0
votes
1
reply
767
views
TFBSTools and readFASTA
TFBSTools
DNASeqData
readFASTA
DNA
RStudio
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
HELEN
• 0
0
votes
0
replies
624
views
TFBSTools- analysis for trascriprion factors
TFBSTools
RStudio
R
2.5 years ago
HELEN
• 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
0
votes
1
reply
2.2k
views
Unable to Install packages in R
rstudio
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Fiona
• 0
0
votes
4
replies
3.0k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq
rstudio
fasta
Biostrings
csv
2.7 years ago
HELEN
• 0
5
votes
15
replies
11k
views
Can't able to install Seurat in Rstudio
Rstudio
Seurat
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
KOUSTAV
• 0
1
vote
7
replies
2.9k
views
Error with hclust
dendrogram
hclust
textanalysis
R
RStudio
3.1 years ago • updated 3.0 years ago
Abby
▴ 10
0
votes
1
reply
844
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups
RStudio
DECIPHER
Specificprimers
updated 3.2 years ago by
Erik Wright
▴ 150 • written 3.2 years ago by
noeliaruizalonso23
• 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
Michael Lawrence
★ 11k • written 3.4 years ago by
Søren
• 0
0
votes
1
reply
937
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 4.2 years ago by
shepherl
3.9k • written 4.2 years ago by
bwiley4
• 0
0
votes
5
replies
1.5k
views
readTranscriptFeatures from genomation
R
Rstudio
Error
readTranscriptFeatures
genomation
updated 4.5 years ago by
altuna akalin
▴ 20 • written 4.5 years ago by
hwaterma
• 0
2
votes
1
reply
8.4k
views
Error: status was 'SSL connect error'
bioconductor
proxy
macOS
R
RStudio
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
mcall
▴ 20
0
votes
5
replies
1.6k
views
Using RStudio AMI with localhost
RStudio
AWS
AMI
4.8 years ago
bio-explorer
• 0
3
votes
6
replies
1.8k
views
Integer overflow issue with ChIPQC
ChIPQC
Rstudio
updated 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
Nitesh Kumar Singh
▴ 30
1
vote
8
replies
2.7k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2
null
summarizedexperiment
rstudio
updated 4.9 years ago by
Martin Morgan
25k • written 4.9 years ago by
200dumplings
• 0
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
5.1 years ago
fatimarasool135
• 0
0
votes
4
replies
1.6k
views
New computer won't install DESeq2
deseq2
rstudio
install error
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
jyoung
• 0
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
James W. MacDonald
65k • written 5.7 years ago by
austin.taylor
• 0
0
votes
1
reply
1.2k
views
Install Bioconductor package locally/temporarily
R
rstudio
package installation
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
ariel
▴ 20
0
votes
1
reply
1.9k
views
DeSeq2 installation on ubuntu fails
deseq2
R
ubuntu
bioconductor
rstudio
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
drumarsohail
• 0
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
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
Mike Smith
★ 6.5k • written 6.2 years ago by
mullpaul
• 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
James W. MacDonald
65k • written 6.2 years ago by
biostR
▴ 10
0
votes
2
replies
3.6k
views
Error in file.choose() : file choice cancelled
package development
bioconductor
rstudio
rmarkdown
vignettes
6.5 years ago
clarisbaby
• 0
1
vote
2
replies
1.3k
views
Rstudio session aborts when using read.celfiles()
oligo package
Rstudio
fatal error
microarray
CEL
6.5 years ago
biostR
▴ 10
0
votes
0
replies
1.6k
views
Problem with heatmap by ComplexHeatmap
complexheatmap
Rstudio
NOISeq
6.6 years ago
Luiz
• 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
Martin Morgan
25k • written 6.8 years ago by
yog312
• 0
1
vote
1
reply
4.9k
views
MA plot in R
rstudio
r
plotMA
6.9 years ago
g.k
• 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
1.4k
views
problem in installing flowclust
rstudio
flowclust
updated 6.9 years ago by
shepherl
3.9k • written 6.9 years ago by
shadhiksk
• 0
0
votes
1
reply
1.2k
views
can a function outliers be applied for a flowframe?
bioconductor
flow cytometry
rstudio
updated 6.9 years ago by
SamGG
▴ 350 • written 6.9 years ago by
shadhiksk
• 0
50 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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