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RStudio
•
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0
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7
replies
1.6k
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 9 months ago by
swbarnes2
★ 1.4k • written 9 months ago by
Aaliya
• 0
0
votes
0
replies
479
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 13 months ago by
James W. MacDonald
67k • written 13 months ago by
Ramirj49
• 0
2
votes
3
replies
802
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
14 months ago
R_Page
• 0
0
votes
2
replies
890
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
14 months ago
yee
• 0
1
vote
3
replies
779
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
j_denton
• 0
4
votes
6
replies
2.0k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio
convert
ensembldb
NCBI
updated 4 months ago by
MauriAndres
• 0 • written 15 months ago by
j_denton
• 0
0
votes
7
replies
3.1k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
BioES
• 0
0
votes
1
reply
620
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 17 months ago by
ATpoint
★ 4.6k • written 17 months ago by
DrFizz
• 0
0
votes
1
reply
1.9k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 18 months ago by
ATpoint
★ 4.6k • written 18 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 2.1 years ago by
Christian Mertes
• 0 • written 2.2 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 2.3 years ago by
James W. MacDonald
67k • written 2.3 years ago by
Kevin Coombes
▴ 430
0
votes
1
reply
1.0k
views
Issue with installation of a package.
RStudio
flowFDA
updated 2.3 years ago by
Basti
▴ 780 • written 2.3 years ago by
kinoshamoodley
• 0
0
votes
14
replies
5.2k
views
GenomeInfoDbData had non-zero exit status
DESeq2
RStudio
GenomeInfoDbData
hadnon-zeroexitstatus
updated 2.3 years ago by
wshao9
• 0 • written 2.6 years ago by
JoseR
• 0
4
votes
5
replies
2.9k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 2.8 years ago by
960942
• 0
0
votes
0
replies
1.5k
views
function GDCquery_Maf error
rstudio
maftools
2.8 years ago
misslubblys
• 0
9
votes
14
replies
8.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 6 months ago by
shepherl
4.1k • written 3.0 years ago by
jon.klonowski
▴ 40
0
votes
3
replies
1.8k
views
Reading large file (15GB) in R
R
Rstudio
Bioconducter
statistics
updated 2.9 years ago by
Sean Davis
21k • written 3.0 years ago by
Jitendra
▴ 10
0
votes
0
replies
795
views
Read the first sequence from fasta file - TFBSTool
TFBSTools
FASTA
RStudio
3.2 years ago
HELEN
• 0
0
votes
1
reply
1.0k
views
TFBSTools and readFASTA
TFBSTools
DNASeqData
readFASTA
DNA
RStudio
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
HELEN
• 0
0
votes
0
replies
788
views
TFBSTools- analysis for trascriprion factors
TFBSTools
RStudio
R
3.3 years ago
HELEN
• 0
1
vote
5
replies
2.8k
views
DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2
RStudio
3.3 years ago
Sonia
• 0
0
votes
1
reply
2.6k
views
Unable to Install packages in R
rstudio
updated 3.4 years ago by
James W. MacDonald
67k • written 3.4 years ago by
Fiona
• 0
0
votes
4
replies
3.9k
views
transformation of csv file to fasta format with biostrings and r studio
DNASeq
rstudio
fasta
Biostrings
csv
3.4 years ago
HELEN
• 0
5
votes
15
replies
15k
views
Can't able to install Seurat in Rstudio
Rstudio
Seurat
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
KOUSTAV
• 0
1
vote
7
replies
3.9k
views
Error with hclust
dendrogram
hclust
textanalysis
R
RStudio
3.8 years ago
Abby
▴ 10
0
votes
1
reply
1.1k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups
RStudio
DECIPHER
Specificprimers
updated 3.9 years ago by
Erik Wright
▴ 150 • written 4.0 years ago by
noeliaruizalonso23
• 0
1
vote
5
replies
5.4k
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 4.2 years ago by
Michael Lawrence
★ 11k • written 4.2 years ago by
Søren
• 0
0
votes
1
reply
1.2k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 4.9 years ago by
shepherl
4.1k • written 4.9 years ago by
bwiley4
• 0
0
votes
5
replies
2.0k
views
readTranscriptFeatures from genomation
R
Rstudio
Error
readTranscriptFeatures
genomation
updated 5.2 years ago by
altuna akalin
▴ 20 • written 5.2 years ago by
hwaterma
• 0
2
votes
1
reply
10.0k
views
Error: status was 'SSL connect error'
bioconductor
proxy
macOS
R
RStudio
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
mcall
▴ 20
0
votes
5
replies
2.0k
views
Using RStudio AMI with localhost
RStudio
AWS
AMI
5.5 years ago
bio-explorer
• 0
3
votes
6
replies
2.1k
views
Integer overflow issue with ChIPQC
ChIPQC
Rstudio
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
Nitesh Kumar Singh
▴ 30
1
vote
8
replies
3.1k
views
DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
deseq2
null
summarizedexperiment
rstudio
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
200dumplings
• 0
0
votes
0
replies
2.1k
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
5.8 years ago
fatimarasool135
• 0
2
votes
4
replies
2.1k
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
updated 21 months ago by
Shreyash
▴ 10 • written 6.2 years ago by
rtwest
• 0
0
votes
4
replies
1.9k
views
New computer won't install DESeq2
deseq2
rstudio
install error
updated 6.3 years ago by
Michael Love
43k • written 6.3 years ago by
jyoung
• 0
2
votes
2
replies
4.3k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio
heatmap.2
updated 6.5 years ago by
James W. MacDonald
67k • written 6.5 years ago by
austin.taylor
• 0
0
votes
1
reply
1.6k
views
Install Bioconductor package locally/temporarily
R
rstudio
package installation
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
ariel
▴ 20
0
votes
1
reply
2.1k
views
DeSeq2 installation on ubuntu fails
deseq2
R
ubuntu
bioconductor
rstudio
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
drumarsohail
• 0
0
votes
0
replies
1.3k
views
Running ASpli on R results in "Error: vector memory exhausted (limit reached?)"
aspli
rstudio
6.7 years ago
arphatak
• 0
1
vote
4
replies
1.9k
views
biomaRt scan error for latest assembly when indicating version Number
biomart
rstudio
ensembl mart
updated 6.9 years ago by
Mike Smith
★ 6.6k • written 6.9 years ago by
mullpaul
• 0
2
votes
4
replies
1.5k
views
R session terminates when trying to load affycoretools package
affycoretools
Rstudio
fatal error
updated 6.9 years ago by
James W. MacDonald
67k • written 6.9 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
7.2 years ago
clarisbaby
• 0
1
vote
2
replies
1.6k
views
Rstudio session aborts when using read.celfiles()
oligo package
Rstudio
fatal error
microarray
CEL
7.2 years ago
biostR
▴ 10
0
votes
0
replies
1.8k
views
Problem with heatmap by ComplexHeatmap
complexheatmap
Rstudio
NOISeq
7.4 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 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
yog312
• 0
1
vote
1
reply
5.2k
views
MA plot in R
rstudio
r
plotMA
7.6 years ago
g.k
• 0
0
votes
3
replies
2.9k
views
error installing cummeRbund in R studio (Windows desktop)
Rstudio
cummerbund
error
7.6 years ago
mszskb
• 0
0
votes
4
replies
1.7k
views
problem in installing flowclust
rstudio
flowclust
updated 7.7 years ago by
shepherl
4.1k • written 7.7 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 7.7 years ago by
SamGG
▴ 360 • written 7.7 years ago by
shadhiksk
• 0
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Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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