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XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
6
votes
10
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2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.8k • written 4 months ago by ▴ 10
0
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0
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259
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[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
5 months ago Anke • 0
1
vote
1
reply
550
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 6 months ago by 68k • written 7 months ago by • 0
2
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3
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703
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 months ago by • 0
3
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3
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15k
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How to fix 'long vectors not supported yet' error in R
r
updated 12 months ago by • 0 • written 6.1 years ago by • 0
0
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0
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389
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Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
13 months ago danalvoronov ▴ 10
0
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4
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862
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limma with interaction term
R biostatistics limma Epigenetics
13 months ago Jitendra ▴ 10
0
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3
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2.2k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 4.1 years ago by • 0
1
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5
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2.6k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.1 years ago by ▴ 10
0
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7
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2.2k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 16 months ago by • 0
0
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0
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537
views
multipollutant models
statistics Regression r limma
16 months ago Jitendra ▴ 10
3
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4
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1.1k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
16 months ago pl23 • 0
1
vote
3
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2.3k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 16 months ago by ▴ 750 • written 3.9 years ago by • 0
0
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10
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1.5k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
16 months ago • updated 13 months ago ScafioRuo • 0
12
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10
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14k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 12 months ago by • 0 • written 17 months ago by ▴ 20
0
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2
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994
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
19 months ago yr542 • 0
1
vote
2
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1.1k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
20 months ago Miguel • 0
2
votes
5
replies
1.8k
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
20 months ago mohammedtoufiq91 ▴ 10
0
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1
reply
826
views
Gene enrichment analysis
analysis R GOfuncR
updated 21 months ago by ▴ 760 • written 21 months ago by • 0
0
votes
2
replies
1.7k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 22 months ago by • 0 • written 4.1 years ago by • 0
0
votes
1
reply
948
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 23 months ago by 52k • written 23 months ago by • 0
0
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1
reply
753
views
DEseq2 Single cell data paired design
R
updated 23 months ago by ▴ 30 • written 23 months ago by • 0
0
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4
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1.5k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
1
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3
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1.4k
views
tximport error
tximport r
updated 23 months ago by 43k • written 23 months ago by • 0
1
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2
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1.4k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
23 months ago Abdul ▴ 20
0
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0
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751
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
23 months ago aymanreffai • 0
1
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1
reply
2.6k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 23 months ago by ★ 4.1k • written 23 months ago by ▴ 10
0
votes
4
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1.4k
views
Unable to install BiocManager
Biocmanager R
updated 23 months ago by ▴ 50 • written 23 months ago by • 0
1
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1
reply
1.9k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 2.0 years ago by • 0 • written 2.0 years ago by • 0
0
votes
13
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10k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.0 years ago Laia ▴ 10
1
vote
3
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7.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 2.0 years ago by ★ 4.1k • written 2.1 years ago by ▴ 10
0
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1
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1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.0 years ago by ▴ 750 • written 2.0 years ago by ▴ 10
0
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0
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734
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rDGIdb package: score of the results
rDGIdb r
2.0 years ago HELEN • 0
2
votes
1
reply
751
views
add column with name in R
name R column
updated 2.1 years ago by ▴ 70 • written 2.1 years ago by • 0
0
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4
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1.5k
views
how to extract list in quantile in R
R quantile list
2.1 years ago sat • 0
0
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0
replies
1.0k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
2.1 years ago Manav • 0
0
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0
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843
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
2.1 years ago Jitendra ▴ 10
3
votes
2
replies
1.3k
views
how to extract and match information of two filein R
R column match
2.1 years ago sat • 0
0
votes
0
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783
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
2.1 years ago info ▴ 10
0
votes
17
replies
2.4k
views
How to check linear model
modalmatrix limma R linear
2.1 years ago Jitendra ▴ 10
0
votes
1
reply
1.1k
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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3
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1.7k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 2.1 years ago by ▴ 760 • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
2.1 years ago abhisek001 • 0
0
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4
replies
1.4k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
2.1 years ago Dr. • 0
0
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1
reply
1.6k
views
Extract Intersection Values from Venn
R Venn
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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6
replies
2.5k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.1 years ago yr542 • 0
0
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0
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768
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.1 years ago Luomeng • 0
2
votes
9
replies
1.8k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 2.1 years ago by 68k • written 2.2 years ago by • 0
1
vote
2
replies
4.0k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
50 results • Page 1 of 1
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Comment: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati by Mei • 0
I have a similar experiment with 7 paired samples (T0 and T1) in each of 4 outcome groups. I am using RUVr combined with limma-voom, so I a…
Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
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Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
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