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r
•
reset
0
votes
0
replies
77
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
18 days ago
danalvoronov
▴ 10
0
votes
4
replies
265
views
limma with interaction term
R
biostatistics
limma
Epigenetics
5 weeks ago • updated 22 days ago
Jitendra
▴ 10
0
votes
3
replies
1.5k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.1 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 9.1 years ago by
chandlerjd58
▴ 10
0
votes
3
replies
405
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 3 months ago by
daenerystargaryen56
• 0 • written 3 months ago by
Sitapriya
• 0
0
votes
0
replies
167
views
multipollutant models
statistics
Regression
r
limma
3 months ago
Jitendra
▴ 10
3
votes
4
replies
453
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
3 months ago
pl23
• 0
1
vote
3
replies
1.3k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 4 months ago by
Robert Ivanek
▴ 730 • written 2.9 years ago by
ltzhou
• 0
0
votes
10
replies
706
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
4 months ago • updated 17 days ago
ScafioRuo
• 0
10
votes
7
replies
5.2k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 7 weeks ago by
Mike Smith
★ 6.4k • written 4 months ago by
Abhishek
▴ 10
0
votes
2
replies
495
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
7 months ago • updated 6 months ago
yr542
• 0
1
vote
2
replies
535
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
7 months ago
Miguel
• 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
8 months ago • updated 7 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
458
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 9 months ago by
Lluís Revilla Sancho
▴ 730 • written 9 months ago by
Eliza
• 0
0
votes
2
replies
1.1k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 9 months ago by
hfbarrerat
• 0 • written 3.1 years ago by
Bethan
• 0
0
votes
1
reply
570
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
qiz218591
• 0
0
votes
1
reply
463
views
DEseq2 Single cell data paired design
R
updated 10 months ago by
Marek Gierlinski
▴ 30 • written 10 months ago by
Caro
• 0
0
votes
4
replies
789
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 10 months ago by
swbarnes2
★ 1.3k • written 10 months ago by
Young Tae
• 0
1
vote
3
replies
754
views
tximport error
tximport
r
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Joana
• 0
1
vote
2
replies
800
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
11 months ago
Abdul
▴ 20
0
votes
0
replies
437
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
11 months ago
aymanreffai
• 0
1
vote
1
reply
1.1k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 11 months ago by
morgan.sobol
• 0
0
votes
4
replies
798
views
Unable to install BiocManager
Biocmanager
R
updated 11 months ago by
L
▴ 50 • written 11 months ago by
sidrah19220
• 0
1
vote
1
reply
1.1k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 11 months ago by
Cynthia
• 0 • written 12 months ago by
Nargil
• 0
0
votes
13
replies
3.9k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
12 months ago
Laia
▴ 10
0
votes
3
replies
3.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 13 months ago by
YNKIM
• 0
0
votes
1
reply
649
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 12 months ago by
Peter Hickey
▴ 670 • written 12 months ago by
cathalgking
▴ 10
0
votes
0
replies
434
views
rDGIdb package: score of the results
rDGIdb
r
12 months ago
HELEN
• 0
2
votes
1
reply
483
views
add column with name in R
name
R
column
updated 12 months ago by
helucro
▴ 70 • written 12 months ago by
sat
• 0
0
votes
4
replies
791
views
how to extract list in quantile in R
R
quantile
list
12 months ago
sat
• 0
0
votes
0
replies
480
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
12 months ago
Manav
• 0
0
votes
0
replies
503
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics
R
Bioconducter
12 months ago
Jitendra
▴ 10
3
votes
2
replies
747
views
how to extract and match information of two filein R
R
column
match
12 months ago
sat
• 0
0
votes
0
replies
453
views
News:
Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics
R
Bioconductor
MassSpectrometry
12 months ago
info
▴ 10
0
votes
17
replies
1.6k
views
How to check linear model
modalmatrix
limma
R
linear
13 months ago • updated 12 months ago
Jitendra
▴ 10
0
votes
1
reply
694
views
customised help function in argparse() in R
command-line
R
command-line-arguments
argparse()
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Learner
• 0
0
votes
3
replies
852
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 13 months ago by
Lluís Revilla Sancho
▴ 730 • written 13 months ago by
Jitendra
▴ 10
1
vote
2
replies
779
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData
R
microbiomeutilities
Install
13 months ago
abhisek001
• 0
0
votes
4
replies
876
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
13 months ago
Dr.
• 0
0
votes
1
reply
777
views
Extract Intersection Values from Venn
R
Venn
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Dr.
• 0
2
votes
6
replies
1.6k
views
DMRcate
DMRcate
R
DMRcatedata
Markdown
13 months ago
yr542
• 0
0
votes
0
replies
488
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
13 months ago
Luomeng
• 0
2
votes
9
replies
1.2k
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Berna
• 0
0
votes
2
replies
1.5k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 13 months ago by
Gordon Smyth
50k • written 14 months ago by
Keith
• 0
0
votes
3
replies
840
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
sat
• 0
0
votes
1
reply
592
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 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Элина
• 0
0
votes
2
replies
676
views
TnSeq as ZINB? Alternatives in R?
DESeq2
R
edgeR
Python
TnSeq
updated 15 months ago by
chaco001
• 0 • written 16 months ago by
David R
▴ 90
2
votes
4
replies
2.0k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 15 months ago by
abhisek001
• 0
0
votes
1
reply
615
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2
MultipleComparison
r
updated 15 months ago by
Michael Love
41k • written 15 months ago by
ncorak
• 0
4
votes
6
replies
1.1k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
15 months ago
Abdul
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Comment: BioC2024 abstract submission is open!
by
howell
• 0
What are the conditions for approval of people in difficult circumstances? I want this scholarship
Comment: European Bioconductor Conference 2023 planning
by
william
• 0
[@MariaDoyle][1] Without a doubt. In that position, I will be included in the discussion. [1]: https://support.bioconductor.org/u/239…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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