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6
votes
10
replies
2.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 days ago by ★ 4.6k • written 25 days ago by ▴ 10
0
votes
0
replies
181
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
10 weeks ago Anke • 0
1
vote
1
reply
406
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 3 months ago by 67k • written 3 months ago by • 0
2
votes
3
replies
589
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 5 months ago by • 0
3
votes
3
replies
15k
views
How to fix 'long vectors not supported yet' error in R
r
updated 8 months ago by • 0 • written 5.9 years ago by • 0
0
votes
0
replies
328
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
9 months ago danalvoronov ▴ 10
0
votes
4
replies
720
views
limma with interaction term
R biostatistics limma Epigenetics
10 months ago Jitendra ▴ 10
0
votes
3
replies
2.0k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.8 years ago by • 0
1
vote
5
replies
2.5k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.9 years ago by ▴ 10
0
votes
7
replies
2.0k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 12 months ago by • 0
0
votes
0
replies
476
views
multipollutant models
statistics Regression r limma
12 months ago Jitendra ▴ 10
3
votes
4
replies
967
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
13 months ago pl23 • 0
1
vote
3
replies
2.0k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 13 months ago by ▴ 750 • written 3.6 years ago by • 0
0
votes
10
replies
1.3k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
13 months ago • updated 9 months ago ScafioRuo • 0
12
votes
10
replies
13k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 9 months ago by • 0 • written 14 months ago by ▴ 20
0
votes
2
replies
864
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
16 months ago • updated 15 months ago yr542 • 0
1
vote
2
replies
981
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
17 months ago Miguel • 0
2
votes
5
replies
1.7k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
17 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
748
views
Gene enrichment analysis
analysis R GOfuncR
updated 18 months ago by ▴ 760 • written 18 months ago by • 0
0
votes
2
replies
1.6k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 19 months ago by • 0 • written 3.8 years ago by • 0
0
votes
1
reply
871
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 20 months ago by 52k • written 20 months ago by • 0
0
votes
1
reply
694
views
DEseq2 Single cell data paired design
R
updated 20 months ago by ▴ 30 • written 20 months ago by • 0
0
votes
4
replies
1.3k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 20 months ago by 43k • written 20 months ago by • 0
1
vote
2
replies
1.3k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
20 months ago Abdul ▴ 20
0
votes
0
replies
685
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
20 months ago aymanreffai • 0
1
vote
1
reply
2.1k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 20 months ago by ★ 4.1k • written 20 months ago by ▴ 10
0
votes
4
replies
1.2k
views
Unable to install BiocManager
Biocmanager R
updated 20 months ago by ▴ 50 • written 20 months ago by • 0
1
vote
1
reply
1.7k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 21 months ago by • 0 • written 21 months ago by • 0
0
votes
13
replies
8.1k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
21 months ago Laia ▴ 10
1
vote
3
replies
6.3k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 21 months ago by ★ 4.1k • written 22 months ago by ▴ 10
0
votes
1
reply
1.1k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 21 months ago by ▴ 740 • written 21 months ago by ▴ 10
0
votes
0
replies
676
views
rDGIdb package: score of the results
rDGIdb r
21 months ago HELEN • 0
2
votes
1
reply
684
views
add column with name in R
name R column
updated 21 months ago by ▴ 70 • written 21 months ago by • 0
0
votes
4
replies
1.3k
views
how to extract list in quantile in R
R quantile list
21 months ago sat • 0
0
votes
0
replies
892
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
21 months ago Manav • 0
0
votes
0
replies
754
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
22 months ago Jitendra ▴ 10
3
votes
2
replies
1.1k
views
how to extract and match information of two filein R
R column match
22 months ago sat • 0
0
votes
0
replies
718
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
22 months ago info ▴ 10
0
votes
17
replies
2.2k
views
How to check linear model
modalmatrix limma R linear
22 months ago Jitendra ▴ 10
0
votes
1
reply
979
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 22 months ago by 67k • written 22 months ago by • 0
0
votes
3
replies
1.5k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 22 months ago by ▴ 760 • written 22 months ago by ▴ 10
1
vote
2
replies
1.2k
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
22 months ago abhisek001 • 0
0
votes
4
replies
1.3k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
22 months ago Dr. • 0
0
votes
1
reply
1.3k
views
Extract Intersection Values from Venn
R Venn
updated 22 months ago by 67k • written 22 months ago by • 0
2
votes
6
replies
2.2k
views
DMRcate
DMRcate R DMRcatedata Markdown
22 months ago yr542 • 0
0
votes
0
replies
711
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
22 months ago Luomeng • 0
2
votes
9
replies
1.6k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 22 months ago by 67k • written 22 months ago by • 0
1
vote
2
replies
3.3k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 22 months ago by 52k • written 23 months ago by • 0
0
votes
3
replies
1.3k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 23 months ago by 67k • written 23 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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