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R
•
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0
votes
2
replies
201
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
7 weeks ago • updated 21 days ago
yr542
• 0
1
vote
2
replies
205
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 weeks ago
Miguel
• 0
2
votes
5
replies
509
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
269
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 3 months ago by
Lluís Revilla Sancho
▴ 720 • written 3 months ago by
Eliza
• 0
0
votes
2
replies
866
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 4 months ago by
hfbarrerat
• 0 • written 2.6 years ago by
Bethan
• 0
0
votes
1
reply
340
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 5 months ago by
Gordon Smyth
48k • written 5 months ago by
qiz218591
• 0
0
votes
1
reply
274
views
DEseq2 Single cell data paired design
R
updated 5 months ago by
Marek Gierlinski
▴ 10 • written 5 months ago by
Caro
• 0
0
votes
4
replies
397
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Young Tae
• 0
1
vote
3
replies
412
views
tximport error
tximport
r
updated 5 months ago by
Michael Love
40k • written 5 months ago by
Joana
• 0
1
vote
2
replies
486
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
5 months ago
Abdul
▴ 20
0
votes
0
replies
221
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ
R
DEP
error
5 months ago
aymanreffai
• 0
1
vote
1
reply
491
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 5 months ago by
Guido Hooiveld
★ 3.7k • written 5 months ago by
morgan.sobol
• 0
0
votes
4
replies
445
views
Unable to install BiocManager
Biocmanager
R
updated 5 months ago by
L
▴ 50 • written 5 months ago by
sidrah19220
• 0
1
vote
1
reply
629
views
Error in h5checktype(). H5Identifier not valid.
rhdf5
rhdf
r
updated 6 months ago by
Cynthia
• 0 • written 6 months ago by
Nargil
• 0
0
votes
13
replies
1.7k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
6 months ago
Laia
▴ 10
0
votes
3
replies
1.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot
R
clusterProfiler
updated 6 months ago by
Guido Hooiveld
★ 3.7k • written 7 months ago by
YNKIM
• 0
0
votes
1
reply
333
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 6 months ago by
Peter Hickey
▴ 650 • written 6 months ago by
cathalgking
▴ 10
0
votes
0
replies
251
views
rDGIdb package: score of the results
rDGIdb
r
6 months ago
HELEN
• 0
2
votes
1
reply
296
views
add column with name in R
name
R
column
updated 6 months ago by
helucro
▴ 70 • written 6 months ago by
sat
• 0
0
votes
4
replies
432
views
how to extract list in quantile in R
R
quantile
list
6 months ago
sat
• 0
0
votes
0
replies
274
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
6 months ago
Manav
• 0
0
votes
0
replies
269
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics
R
Bioconducter
7 months ago
Jitendra
▴ 10
3
votes
2
replies
380
views
how to extract and match information of two filein R
R
column
match
7 months ago
sat
• 0
0
votes
0
replies
245
views
News:
Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics
R
Bioconductor
MassSpectrometry
7 months ago
info
▴ 10
0
votes
17
replies
1.0k
views
How to check linear model
modalmatrix
limma
R
linear
7 months ago
Jitendra
▴ 10
0
votes
1
reply
376
views
customised help function in argparse() in R
command-line
R
command-line-arguments
argparse()
updated 7 months ago by
James W. MacDonald
63k • written 7 months ago by
Learner
• 0
0
votes
3
replies
526
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 7 months ago by
Lluís Revilla Sancho
▴ 720 • written 7 months ago by
Jitendra
▴ 10
1
vote
2
replies
458
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData
R
microbiomeutilities
Install
7 months ago
abhisek001
• 0
0
votes
4
replies
532
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
7 months ago
Dr.
• 0
0
votes
1
reply
418
views
Extract Intersection Values from Venn
R
Venn
updated 7 months ago by
James W. MacDonald
63k • written 7 months ago by
Dr.
• 0
2
votes
6
replies
868
views
DMRcate
DMRcate
R
DMRcatedata
Markdown
7 months ago
yr542
• 0
0
votes
0
replies
284
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
7 months ago
Luomeng
• 0
2
votes
9
replies
809
views
mas5calls function doesn't work; mirna40cdf problem
R
Bioconductor
mas5calls
updated 7 months ago by
James W. MacDonald
63k • written 7 months ago by
Berna
• 0
0
votes
2
replies
725
views
R: Confused about Limma R package output being LogFC or Log2FC
limma
R
ExpressionData
updated 7 months ago by
Gordon Smyth
48k • written 8 months ago by
Keith
• 0
0
votes
3
replies
507
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures
R
genomation
bed
updated 8 months ago by
James W. MacDonald
63k • written 8 months ago by
sat
• 0
0
votes
1
reply
368
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 8 months ago by
Gordon Smyth
48k • written 8 months ago by
Элина
• 0
0
votes
2
replies
511
views
TnSeq as ZINB? Alternatives in R?
DESeq2
R
edgeR
Python
TnSeq
updated 9 months ago by
chaco001
• 0 • written 10 months ago by
David R
▴ 70
2
votes
4
replies
1.2k
views
question regarding installation of "enrichplot" with BiocManager
R
BiocManager
install
clusterProfiler
GO
written 10 months ago by
abhisek001
• 0
0
votes
1
reply
450
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2
MultipleComparison
r
updated 9 months ago by
Michael Love
40k • written 9 months ago by
ncorak
• 0
4
votes
6
replies
741
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
9 months ago
Abdul
▴ 20
1
vote
2
replies
5.1k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 9 months ago by
snijesh
▴ 20 • written 5.8 years ago by
p_donchev84
• 0
0
votes
3
replies
661
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 9 months ago by
Erik Wright
▴ 150 • written 9 months ago by
Nelli
• 0
4
votes
8
replies
1.3k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 4 months ago by
Gordon Smyth
48k • written 10 months ago by
Sabiha
▴ 20
1
vote
2
replies
518
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
10 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
455
views
ape::dnds produces nan value
R
ape
dnds
nan
nanotubes
10 months ago • updated 9 months ago
Working
• 0
0
votes
2
replies
639
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 10 months ago by
ATpoint
★ 3.4k • written 10 months ago by
lola
• 0
2
votes
4
replies
2.1k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
10 months ago
mohammedtoufiq91
▴ 10
1
vote
7
replies
843
views
query regarding error in installation of "goseq" R bioconductor package
R
Bioconductor
Install
updated 10 months ago by
shepherl
3.5k • written 10 months ago by
abhisek001
• 0
0
votes
2
replies
456
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization
R
cqn
10 months ago
Sally
• 0
1
vote
2
replies
522
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
10 months ago
mohammedtoufiq91
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of
by
Gregory
• 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Votes
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
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