Showing : R • reset
0
votes
2
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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 ▴ 720 • written 3 months ago by • 0
0
votes
2
replies
866
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 4 months ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
340
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 5 months ago by 48k • written 5 months ago by • 0
0
votes
1
reply
274
views
DEseq2 Single cell data paired design
R
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
0
votes
4
replies
397
views
Combine RNA-seq
BatchEffect R rnaseq
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
1
vote
3
replies
412
views
tximport error
tximport r
updated 5 months ago by 40k • written 5 months ago by • 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 ★ 3.7k • written 5 months ago by • 0
0
votes
4
replies
445
views
Unable to install BiocManager
Biocmanager R
updated 5 months ago by ▴ 50 • written 5 months ago by • 0
1
vote
1
reply
629
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 6 months ago by • 0 • written 6 months ago by • 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 ★ 3.7k • written 7 months ago by • 0
0
votes
1
reply
333
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 6 months ago by ▴ 650 • written 6 months ago by ▴ 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 ▴ 70 • written 6 months ago by • 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 63k • written 7 months ago by • 0
0
votes
3
replies
526
views
batch effect in EPIC array data
statistics Epigenetics R
updated 7 months ago by ▴ 720 • written 7 months ago by ▴ 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 63k • written 7 months ago by • 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 63k • written 7 months ago by • 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 48k • written 8 months ago by • 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 63k • written 8 months ago by • 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 48k • written 8 months ago by • 0
0
votes
2
replies
511
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 9 months ago by • 0 • written 10 months ago by ▴ 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 • 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 40k • written 9 months ago by • 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 ▴ 20 • written 5.8 years ago by • 0
0
votes
3
replies
661
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 9 months ago by ▴ 150 • written 9 months ago by • 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 48k • written 10 months ago by ▴ 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 ★ 3.4k • written 10 months ago by • 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 3.5k • written 10 months ago by • 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
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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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