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r
•
reset
0
votes
0
replies
110
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
7 weeks ago
danalvoronov
▴ 10
0
votes
4
replies
344
views
limma with interaction term
R
biostatistics
limma
Epigenetics
10 weeks ago • updated 8 weeks ago
Jitendra
▴ 10
0
votes
3
replies
472
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 4 months ago by
Sitapriya
• 0
0
votes
0
replies
216
views
multipollutant models
statistics
Regression
r
limma
4 months ago
Jitendra
▴ 10
3
votes
4
replies
517
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
0
votes
10
replies
792
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 7 weeks ago
ScafioRuo
• 0
10
votes
10
replies
6.7k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 5 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
2
replies
543
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
591
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
1.3k
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
505
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
1
reply
623
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 11 months ago by
Gordon Smyth
50k • written 12 months ago by
qiz218591
• 0
0
votes
1
reply
490
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
882
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
849
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
1
vote
2
replies
872
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
12 months ago
Abdul
▴ 20
0
votes
0
replies
475
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
12 months ago
aymanreffai
• 0
0
votes
4
replies
870
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 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
13
replies
4.6k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
13 months ago
Laia
▴ 10
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
1
reply
718
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
461
views
rDGIdb package: score of the results
rDGIdb
r
13 months ago
HELEN
• 0
2
votes
1
reply
510
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
850
views
how to extract list in quantile in R
R
quantile
list
13 months ago
sat
• 0
0
votes
0
replies
537
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
13 months ago
Manav
• 0
0
votes
0
replies
550
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
791
views
how to extract and match information of two filein R
R
column
match
14 months ago
sat
• 0
0
votes
0
replies
498
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
3
replies
933
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
0
votes
1
reply
728
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
1
vote
2
replies
830
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData
R
microbiomeutilities
Install
14 months ago
abhisek001
• 0
0
votes
3
replies
3.7k
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
4
replies
942
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
14 months ago
Dr.
• 0
0
votes
1
reply
864
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
528
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
14 months ago
Luomeng
• 0
2
votes
9
replies
1.2k
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Berna
• 0
0
votes
2
replies
1.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 14 months ago by
Gordon Smyth
50k • written 15 months ago by
Keith
• 0
0
votes
3
replies
907
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
639
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 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Элина
• 0
4
votes
6
replies
1.2k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
16 months ago
Abdul
▴ 20
0
votes
1
reply
658
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 16 months ago by
ncorak
• 0
0
votes
3
replies
1.0k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 16 months ago by
Erik Wright
▴ 150 • written 16 months ago by
Nelli
• 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 16 months ago by
Sabiha
▴ 20
1
vote
2
replies
781
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
707
views
ape::dnds produces nan value
R
ape
dnds
nan
nanotubes
17 months ago • updated 16 months ago
Working
• 0
2
votes
4
replies
3.4k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
17 months ago
mohammedtoufiq91
▴ 10
1
vote
7
replies
1.4k
views
query regarding error in installation of "goseq" R bioconductor package
R
Bioconductor
Install
updated 17 months ago by
shepherl
3.8k • written 17 months ago by
abhisek001
• 0
50 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
SamGG
▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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