Showing : r • reset
0
votes
0
replies
105
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
7 weeks ago danalvoronov ▴ 10
0
votes
4
replies
323
views
limma with interaction term
R biostatistics limma Epigenetics
9 weeks ago • updated 7 weeks ago Jitendra ▴ 10
0
votes
3
replies
458
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
206
views
multipollutant models
statistics Regression r limma
4 months ago Jitendra ▴ 10
3
votes
4
replies
510
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
4 months ago pl23 • 0
0
votes
10
replies
784
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
5 months ago • updated 6 weeks ago ScafioRuo • 0
10
votes
10
replies
6.4k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 28 days ago by • 0 • written 5 months ago by ▴ 10
0
votes
2
replies
532
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
1
vote
2
replies
577
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
8 months ago Miguel • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago • updated 8 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
501
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
1
reply
613
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
1
reply
486
views
DEseq2 Single cell data paired design
R
updated 11 months ago by ▴ 30 • written 11 months ago by • 0
0
votes
4
replies
868
views
Combine RNA-seq
BatchEffect R rnaseq
updated 11 months ago by ★ 1.3k • written 12 months ago by • 0
1
vote
3
replies
831
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
1
vote
2
replies
858
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
0
votes
0
replies
466
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
12 months ago aymanreffai • 0
0
votes
4
replies
855
views
Unable to install BiocManager
Biocmanager R
updated 12 months ago by ▴ 50 • written 12 months ago by • 0
1
vote
1
reply
1.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
0
votes
13
replies
4.5k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
1
vote
1
reply
1.2k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 12 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
710
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
0
votes
0
replies
456
views
rDGIdb package: score of the results
rDGIdb r
13 months ago HELEN • 0
2
votes
1
reply
508
views
add column with name in R
name R column
updated 13 months ago by ▴ 70 • written 13 months ago by • 0
0
votes
4
replies
829
views
how to extract list in quantile in R
R quantile list
13 months ago sat • 0
0
votes
0
replies
519
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
13 months ago Manav • 0
0
votes
0
replies
542
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
13 months ago Jitendra ▴ 10
3
votes
2
replies
785
views
how to extract and match information of two filein R
R column match
13 months ago sat • 0
0
votes
0
replies
487
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
13 months ago info ▴ 10
0
votes
17
replies
1.6k
views
How to check linear model
modalmatrix limma R linear
14 months ago • updated 13 months ago Jitendra ▴ 10
0
votes
3
replies
910
views
batch effect in EPIC array data
statistics Epigenetics R
updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
0
votes
1
reply
716
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 14 months ago by 65k • written 14 months ago by • 0
1
vote
2
replies
824
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
14 months ago abhisek001 • 0
0
votes
3
replies
3.7k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 13 months ago by ★ 3.9k • written 14 months ago by • 0
0
votes
4
replies
925
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
14 months ago Dr. • 0
0
votes
1
reply
843
views
Extract Intersection Values from Venn
R Venn
updated 14 months ago by 65k • written 14 months ago by • 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
14 months ago yr542 • 0
0
votes
0
replies
517
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
14 months ago Luomeng • 0
2
votes
9
replies
1.2k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 14 months ago by 65k • written 14 months ago by • 0
0
votes
2
replies
1.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 14 months ago by 50k • written 15 months ago by • 0
0
votes
3
replies
893
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
633
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 15 months ago by 50k • written 15 months ago by • 0
4
votes
6
replies
1.2k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
16 months ago Abdul ▴ 20
0
votes
1
reply
649
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 16 months ago by 41k • written 16 months ago by • 0
0
votes
3
replies
1.0k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 16 months ago by ▴ 150 • written 16 months ago by • 0
4
votes
8
replies
2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 months ago by 50k • written 16 months ago by ▴ 20
1
vote
2
replies
772
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
701
views
ape::dnds produces nan value
R ape dnds nan nanotubes
16 months ago Working • 0
2
votes
4
replies
3.4k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
16 months ago mohammedtoufiq91 ▴ 10
1
vote
7
replies
1.4k
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 16 months ago by 3.8k • written 16 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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