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reset
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 29 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
0
replies
116
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
9 weeks ago
danalvoronov
▴ 10
0
votes
4
replies
366
views
limma with interaction term
R
biostatistics
limma
Epigenetics
12 weeks ago • updated 9 weeks ago
Jitendra
▴ 10
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.2 years ago by
tanya
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
0
votes
3
replies
493
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 4 months ago by
daenerystargaryen56
• 0 • written 5 months ago by
Sitapriya
• 0
0
votes
0
replies
233
views
multipollutant models
statistics
Regression
r
limma
5 months ago
Jitendra
▴ 10
3
votes
4
replies
530
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
0
votes
10
replies
810
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 9 weeks ago
ScafioRuo
• 0
10
votes
10
replies
6.9k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 6 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
2
replies
558
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
8 months ago • updated 7 months ago
yr542
• 0
1
vote
2
replies
609
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 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
9 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
518
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Eliza
• 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 11 months ago by
hfbarrerat
• 0 • written 3.2 years ago by
Bethan
• 0
0
votes
1
reply
637
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
qiz218591
• 0
0
votes
1
reply
501
views
DEseq2 Single cell data paired design
R
updated 12 months ago by
Marek Gierlinski
▴ 30 • written 12 months ago by
Caro
• 0
0
votes
4
replies
903
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 12 months ago by
swbarnes2
★ 1.3k • written 12 months ago by
Young Tae
• 0
1
vote
3
replies
864
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
1
vote
2
replies
897
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
12 months ago
Abdul
▴ 20
0
votes
0
replies
484
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
morgan.sobol
• 0
0
votes
4
replies
884
views
Unable to install BiocManager
Biocmanager
R
updated 12 months ago by
L
▴ 50 • written 12 months ago by
sidrah19220
• 0
1
vote
1
reply
1.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 13 months ago by
Cynthia
• 0 • written 13 months ago by
Nargil
• 0
0
votes
13
replies
4.8k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
13 months ago
Laia
▴ 10
0
votes
3
replies
3.8k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 13 months ago by
Guido Hooiveld
★ 3.9k • written 14 months ago by
YNKIM
• 0
0
votes
1
reply
730
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
cathalgking
▴ 10
0
votes
0
replies
467
views
rDGIdb package: score of the results
rDGIdb
r
13 months ago
HELEN
• 0
2
votes
1
reply
519
views
add column with name in R
name
R
column
updated 13 months ago by
helucro
▴ 70 • written 13 months ago by
sat
• 0
0
votes
4
replies
870
views
how to extract list in quantile in R
R
quantile
list
14 months ago
sat
• 0
0
votes
0
replies
552
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
14 months ago
Manav
• 0
0
votes
0
replies
559
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics
R
Bioconducter
14 months ago
Jitendra
▴ 10
3
votes
2
replies
807
views
how to extract and match information of two filein R
R
column
match
14 months ago
sat
• 0
0
votes
0
replies
514
views
News:
Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics
R
Bioconductor
MassSpectrometry
14 months ago
info
▴ 10
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix
limma
R
linear
14 months ago
Jitendra
▴ 10
0
votes
1
reply
734
views
customised help function in argparse() in R
command-line
R
command-line-arguments
argparse()
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Learner
• 0
0
votes
3
replies
947
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 14 months ago by
Lluís Revilla Sancho
▴ 730 • written 14 months ago by
Jitendra
▴ 10
1
vote
2
replies
846
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData
R
microbiomeutilities
Install
14 months ago
abhisek001
• 0
0
votes
4
replies
957
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
14 months ago
Dr.
• 0
0
votes
1
reply
892
views
Extract Intersection Values from Venn
R
Venn
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Dr.
• 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate
R
DMRcatedata
Markdown
14 months ago
yr542
• 0
0
votes
0
replies
536
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
15 months ago
Luomeng
• 0
2
votes
9
replies
1.3k
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Berna
• 0
0
votes
2
replies
1.8k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Keith
• 0
0
votes
3
replies
934
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
sat
• 0
0
votes
1
reply
648
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression
limma
R
TissueMicroarrayData
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Элина
• 0
0
votes
2
replies
723
views
TnSeq as ZINB? Alternatives in R?
DESeq2
R
edgeR
Python
TnSeq
updated 16 months ago by
chaco001
• 0 • written 17 months ago by
David R
▴ 90
2
votes
4
replies
2.1k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 17 months ago by
abhisek001
• 0
0
votes
1
reply
665
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2
MultipleComparison
r
updated 16 months ago by
Michael Love
41k • written 17 months ago by
ncorak
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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