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r
•
reset
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 8 weeks ago by
Amruta
• 0 • written 5.3 years ago by
r.tor
• 0
11
votes
10
replies
7.7k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 9 weeks ago by
juo5
• 0 • written 7 months ago by
Abhishek
▴ 20
0
votes
5
replies
9.4k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 10 weeks ago by
Eva
• 0 • written 7.7 years ago by
ctl
• 0
0
votes
10
replies
869
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
6 months ago • updated 12 weeks ago
ScafioRuo
• 0
0
votes
0
replies
137
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
3 months ago
danalvoronov
▴ 10
0
votes
4
replies
401
views
limma with interaction term
R
biostatistics
limma
Epigenetics
3 months ago
Jitendra
▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 3 months ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
1
vote
12
replies
2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 4 months ago by
Mary
• 0 • written 2.6 years ago by
Ming
▴ 380
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 4 months ago by
Guido Hooiveld
★ 4.0k • written 7.4 years ago by
prp291
• 0
0
votes
3
replies
538
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 5 months ago by
daenerystargaryen56
• 0 • written 5 months ago by
Sitapriya
• 0
1
vote
3
replies
1.9k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 5 months ago by
Rory Stark
★ 5.2k • written 6.7 years ago by
kyliecode
• 0
0
votes
3
replies
1.7k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.3 years ago by
tanya
• 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.3 years ago by
chandlerjd58
▴ 10
0
votes
0
replies
264
views
multipollutant models
statistics
Regression
r
limma
6 months ago
Jitendra
▴ 10
3
votes
4
replies
580
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
6 months ago
pl23
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 6 months ago by
Robert Ivanek
▴ 730 • written 3.1 years ago by
ltzhou
• 0
22
votes
15
replies
7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
0
votes
2
replies
2.1k
views
Creating a qPCRset object from a text file
qPCRset object
nondetects
r
package
txt
updated 7 months ago by
Nat.Nataren
• 0 • written 6.4 years ago by
s.m.may
• 0
7
votes
5
replies
7.2k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 7 months ago by
Ke
• 0 • written 2.1 years ago by
kieran.short
▴ 40
4
votes
5
replies
2.0k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 7 months ago by
jacorvar
▴ 40 • written 19 months ago by
eraldagjika
▴ 20
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 23 months ago by
Mohamed
▴ 30
0
votes
2
replies
594
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
9 months ago • updated 8 months ago
yr542
• 0
1
vote
2
replies
661
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
10 months ago
Miguel
• 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
10 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
540
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 11 months ago by
Lluís Revilla Sancho
▴ 730 • written 11 months ago by
Eliza
• 0
3
votes
3
replies
4.8k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 11 months ago by
Guido Hooiveld
★ 4.0k • written 4.1 years ago by
t.b.kuipers
• 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 12 months ago by
hfbarrerat
• 0 • written 3.3 years ago by
Bethan
• 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 12 months ago by
Gordon Smyth
50k • written 18 months ago by
Sabiha
▴ 20
0
votes
1
reply
1.5k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 12 months ago by
Rob
• 0 • written 5.6 years ago by
owen.donohoe
• 0
0
votes
1
reply
663
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
qiz218591
• 0
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5
r
hdf5
updated 13 months ago by
Yijing
• 0 • written 6.9 years ago by
him4u324
▴ 10
0
votes
1
reply
531
views
DEseq2 Single cell data paired design
R
updated 13 months ago by
Marek Gierlinski
▴ 30 • written 13 months ago by
Caro
• 0
0
votes
4
replies
940
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 13 months ago by
swbarnes2
★ 1.4k • written 13 months ago by
Young Tae
• 0
1
vote
3
replies
916
views
tximport error
tximport
r
updated 13 months ago by
Michael Love
42k • written 13 months ago by
Joana
• 0
2
votes
4
replies
1.7k
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
updated 13 months ago by
Shreyash
▴ 10 • written 5.5 years ago by
rtwest
• 0
1
vote
4
replies
1.4k
views
RNA-seq analysis using R
limma
rnaseq
convert
R
updated 13 months ago by
Gordon Smyth
50k • written 5.5 years ago by
justinkablan225
▴ 10
0
votes
4
replies
951
views
Unable to install BiocManager
Biocmanager
R
updated 13 months ago by
L
▴ 50 • written 13 months ago by
sidrah19220
• 0
1
vote
2
replies
925
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
13 months ago
Abdul
▴ 20
0
votes
0
replies
502
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
13 months ago
aymanreffai
• 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 13 months ago by
Guido Hooiveld
★ 4.0k • written 13 months ago by
morgan.sobol
▴ 10
3
votes
2
replies
2.2k
views
How to do simple Fisher' exact test for overlapped genomic interval in R?
test fisher exact
r
findoverlapsofpeaks
updated 13 months ago by
cherokee1456
• 0 • written 8.4 years ago by
Jurat Shahidin
▴ 80
0
votes
3
replies
1.5k
views
How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r
bioinformatics
peakset
updated 13 months ago by
montuorikandi1759
• 0 • written 8.4 years ago by
Jurat Shahidin
▴ 80
1
vote
1
reply
1.3k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 14 months ago by
Cynthia
• 0 • written 14 months ago by
Nargil
• 0
0
votes
13
replies
5.2k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
14 months ago
Laia
▴ 10
1
vote
3
replies
4.1k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 14 months ago by
Guido Hooiveld
★ 4.0k • written 15 months ago by
YNKIM
▴ 10
0
votes
1
reply
765
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 14 months ago by
Peter Hickey
▴ 740 • written 14 months ago by
cathalgking
▴ 10
0
votes
0
replies
499
views
rDGIdb package: score of the results
rDGIdb
r
14 months ago
HELEN
• 0
2
votes
1
reply
535
views
add column with name in R
name
R
column
updated 14 months ago by
helucro
▴ 70 • written 14 months ago by
sat
• 0
0
votes
4
replies
907
views
how to extract list in quantile in R
R
quantile
list
14 months ago
sat
• 0
0
votes
0
replies
611
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
14 months ago
Manav
• 0
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Comment: How to run allelic imbalance in apeglm
by
parayod376
• 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process")
by
James W. MacDonald
66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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