Showing : r • reset
0
votes
2
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680
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 6 days ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
160
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
0
votes
1
reply
117
views
DEseq2 Single cell data paired design
R
updated 5 weeks ago by ▴ 10 • written 6 weeks ago by • 0
0
votes
4
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218
views
Combine RNA-seq
BatchEffect R rnaseq
updated 6 weeks ago by ★ 1.2k • written 6 weeks ago by • 0
1
vote
3
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188
views
tximport error
tximport r
updated 6 weeks ago by 40k • written 6 weeks ago by • 0
1
vote
2
replies
204
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
7 weeks ago Abdul ▴ 20
0
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0
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95
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
7 weeks ago aymanreffai • 0
0
votes
1
reply
173
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 7 weeks ago by ★ 3.6k • written 7 weeks ago by • 0
0
votes
4
replies
206
views
Unable to install BiocManager
Biocmanager R
updated 7 weeks ago by ▴ 50 • written 7 weeks ago by • 0
1
vote
1
reply
337
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
0
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13
replies
649
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
10 weeks ago Laia ▴ 10
0
votes
3
replies
524
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 11 weeks ago by ★ 3.6k • written 3 months ago by • 0
0
votes
1
reply
164
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 12 weeks ago by ▴ 650 • written 12 weeks ago by ▴ 10
0
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0
replies
94
views
rDGIdb package: score of the results
rDGIdb r
12 weeks ago HELEN • 0
2
votes
1
reply
187
views
add column with name in R
name R column
updated 12 weeks ago by ▴ 70 • written 12 weeks ago by • 0
0
votes
4
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253
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how to extract list in quantile in R
R quantile list
12 weeks ago sat • 0
0
votes
0
replies
99
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
3 months ago Manav • 0
0
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0
replies
135
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
3 months ago Jitendra ▴ 10
3
votes
2
replies
176
views
how to extract and match information of two filein R
R column match
3 months ago sat • 0
0
votes
0
replies
135
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
3 months ago info ▴ 10
0
votes
17
replies
635
views
How to check linear model
modalmatrix limma R linear
3 months ago Jitendra ▴ 10
0
votes
1
reply
184
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 3 months ago by 63k • written 3 months ago by • 0
0
votes
3
replies
257
views
batch effect in EPIC array data
statistics Epigenetics R
updated 3 months ago by ▴ 710 • written 3 months ago by ▴ 10
1
vote
2
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271
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
3 months ago abhisek001 • 0
0
votes
4
replies
272
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
3 months ago Dr. • 0
0
votes
1
reply
208
views
Extract Intersection Values from Venn
R Venn
updated 3 months ago by 63k • written 3 months ago by • 0
2
votes
6
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459
views
DMRcate
DMRcate R DMRcatedata Markdown
3 months ago yr542 • 0
0
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0
replies
126
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
3 months ago Luomeng • 0
2
votes
9
replies
523
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 3 months ago by 63k • written 4 months ago by • 0
0
votes
2
replies
393
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 4 months ago by 47k • written 4 months ago by • 0
0
votes
3
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310
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 4 months ago by 63k • written 4 months ago by • 0
0
votes
1
reply
234
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 4 months ago by 47k • written 4 months ago by • 0
0
votes
2
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375
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 5 months ago by • 0 • written 6 months ago by ▴ 70
2
votes
4
replies
803
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 6 months ago by • 0
0
votes
1
reply
295
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 5 months ago by 40k • written 6 months ago by • 0
4
votes
6
replies
488
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
5 months ago Abdul ▴ 20
1
vote
2
replies
4.7k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 5 months ago by ▴ 20 • written 5.5 years ago by • 0
0
votes
3
replies
441
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 5 months ago by ▴ 150 • written 6 months ago by • 0
4
votes
8
replies
866
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 days ago by 47k • written 6 months ago by ▴ 20
1
vote
2
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359
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
6 months ago mohammedtoufiq91 ▴ 10
0
votes
2
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314
views
ape::dnds produces nan value
R ape dnds nan nanotubes
6 months ago Working • 0
0
votes
2
replies
428
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
2
votes
4
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1.3k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
6 months ago mohammedtoufiq91 ▴ 10
1
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7
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572
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 6 months ago by 3.5k • written 6 months ago by • 0
0
votes
2
replies
280
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
6 months ago Sally • 0
1
vote
2
replies
339
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
4
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473
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
6 months ago Amit Indap ▴ 10
0
votes
2
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442
views
Usinig BiocParallel package in R with M1 MAC
RStudio R M1 BiocParallel Mac
updated 5 months ago by • 0 • written 6 months ago by • 0
2
votes
3
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366
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 6 months ago by 47k • written 6 months ago by • 0
0
votes
1
reply
304
views
Biocparallel Error "Error: BiocParallel errors element index: 1, 2, 3 first error: unable to find an inherited method for function ‘bpbackend’ fo…
R OUTRIDER BiocParallel
updated 5 months ago by • 0 • written 6 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Handling NA's in Deseq2 by Asger Mølgaard • 0
Dear ATpoint Thank you for your response - it works like a charm! You just saved a PhD-study! Thank you :)
Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Votes
C: Minimum number of samples per treatment/group for WGCNA analysis
A: Minimum number of samples per treatment/group for WGCNA analysis
Minimum number of samples per treatment/group for WGCNA analysis
Comment: DESeq2 on multilevel design variable
Comment: Ensembl plants at annotationHub?
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