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RSTUDIO
•
reset
0
votes
5
replies
2.9k
views
New Version of CummeRbund?
cummerbund
rstudio
8.2 years ago
lreiter
• 0
0
votes
20
replies
6.0k
views
SummarizeOverlaps in R
summarizeoverlaps
Bam
rstudio
updated 8.8 years ago by
Jake
▴ 90 • written 8.8 years ago by
Lillyhchen
▴ 10
9
votes
11
replies
5.6k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 5 weeks ago by
shepherl
3.8k • written 2.2 years ago by
jon.klonowski
▴ 40
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
0
votes
4
replies
1.4k
views
problem in installing flowclust
rstudio
flowclust
updated 6.9 years ago by
shepherl
3.8k • written 6.9 years ago by
shadhiksk
• 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
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
5
replies
1.5k
views
readTranscriptFeatures from genomation
R
Rstudio
Error
readTranscriptFeatures
genomation
updated 4.4 years ago by
altuna akalin
▴ 20 • written 4.4 years ago by
hwaterma
• 0
0
votes
9
replies
2.4k
views
is AClust package still available?
Aclust
Aclustering
Rstudio
Clusters
updated 8.7 years ago by
Nitish Kumar Mishra
▴ 40 • written 8.7 years ago by
Lillyhchen
▴ 10
0
votes
3
replies
1.1k
views
Getting annotated and normalized data.
microarray
rstudio
annotation
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
jslow
• 0
1
vote
3
replies
23k
views
Converting first column to rownames
rstudio
8.1 years ago
John
▴ 30
0
votes
3
replies
2.6k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio
cummerbund
error
6.9 years ago • updated 6.8 years ago
mszskb
• 0
0
votes
1
reply
1.1k
views
What preprocessing needs to be done on the Experiment datasets
colon
rstudio
golubesets
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
shramanathakur
• 0
0
votes
2
replies
1.7k
views
Gene symbol annotation not converted for intergenic SNPs with multiple genes
annotation
variantannotation
rstudio
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
noor.suaini
• 0
0
votes
4
replies
2.8k
views
Unable to install Rcpp package for genefo
Rcpp
genefo
linux
linux mint
Rstudio
updated 7.7 years ago by
mfox
• 0 • written 7.7 years ago by
anjali.krishna1008
• 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
Martin Morgan
25k • written 7.2 years ago by
Riot
• 0
0
votes
2
replies
1.1k
views
Problem with cummeRbund
rstudio
cummerbund
7.1 years ago
sanathoi.guru
• 0
2
votes
4
replies
1.6k
views
RStudio quits unexpectedly while running DiffBind on R 3.4.0
software error
diffbind
rstudio
abort
quit
updated 7.0 years ago by
Gord Brown
▴ 650 • written 7.0 years ago by
msabbag2
• 0
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
SamGG
▴ 350 • written 6.9 years ago by
shadhiksk
• 0
0
votes
4
replies
2.9k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq
rstudio
fasta
Biostrings
csv
2.7 years ago • updated 2.6 years ago
HELEN
• 0
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
4
replies
1.6k
views
New computer won't install DESeq2
deseq2
rstudio
install error
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
jyoung
• 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
Martin Morgan
25k • written 4.8 years ago by
200dumplings
• 0
0
votes
1
reply
2.3k
views
Upload error in RStudio running on Amazon - AMI
AMI
RStudio
upload error
custom install
updated 9.3 years ago by
Dan Tenenbaum
★ 8.2k • written 9.3 years ago by
nicholas.provart
• 0
0
votes
3
replies
1.0k
views
how to include System Call Results in Sweave PDF report ?
Sweave
rstudio
updated 9.0 years ago by
Dan Tenenbaum
★ 8.2k • written 9.0 years ago by
a.afshinfard
▴ 10
0
votes
1
reply
1.2k
views
Recent problem with biomaRt query
biomart
biomaRt
R
rstudio
8.8 years ago
nickp60
• 0
0
votes
3
replies
2.1k
views
Getting different results with DESeq2
deseq2
results
rstudio
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
Lillyhchen
▴ 10
1
vote
3
replies
3.5k
views
Problem using display() function on RStudio
display
rstudio
annotationhub
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
barashe
▴ 10
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
Dan Tenenbaum
★ 8.2k • written 8.6 years ago by
svlachavas
▴ 830
3
votes
7
replies
4.5k
views
goseq code after DESeq2 -NO IDEA!
goseq
DESEQ2
RSTUDIO
CODE
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
amyfm
▴ 10
0
votes
2
replies
1.1k
views
Error viewing the data set Golub_Merge
golubEsets
rstudio
updated 8.1 years ago by
James W. MacDonald
65k • written 8.1 years ago by
shramanathakur
• 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
2
votes
1
reply
8.2k
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
1
reply
908
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 4.1 years ago by
shepherl
3.8k • written 4.1 years ago by
bwiley4
• 0
1
vote
7
replies
2.8k
views
Error with hclust
dendrogram
hclust
textanalysis
R
RStudio
3.0 years ago
Abby
▴ 10
1
vote
3
replies
435
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
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
2
votes
18
replies
3.1k
views
edgeR: processAmplicons crashes with large number of hairpins
edger
processamplicons
rstudio
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
thomas.leete
• 0
0
votes
1
reply
746
views
Issue with installation of a package.
RStudio
flowFDA
updated 18 months ago by
Basti
▴ 760 • written 18 months ago by
kinoshamoodley
• 0
2
votes
3
replies
470
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
0
votes
1
reply
740
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
1
reply
813
views
Bug: MOFA2 sets an environment variable that breaks knit in RStudio
RStudio
MOFA2
bug
knitr
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Kevin Coombes
▴ 430
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
5
replies
2.2k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2
RStudio
2.6 years ago • updated 2.5 years ago
Sonia
• 0
0
votes
14
replies
4.0k
views
GenomeInfoDbData had non-zero exit status
DESeq2
RStudio
GenomeInfoDbData
hadnon-zeroexitstatus
updated 18 months ago by
wshao9
• 0 • written 21 months ago by
JoseR
• 0
0
votes
1
reply
961
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
DrFizz
• 0
4
votes
5
replies
2.0k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 24 months ago by
960942
• 0
0
votes
1
reply
375
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
DrFizz
• 0
0
votes
2
replies
328
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
4 months ago
yee
• 0
0
votes
7
replies
1.5k
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 5 months ago by
BioES
• 0
50 results • Page
1 of 1
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Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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