Showing : r • reset
0
votes
0
replies
126
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
11 weeks ago danalvoronov ▴ 10
0
votes
4
replies
393
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
0
votes
3
replies
519
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 5 months ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
244
views
multipollutant models
statistics Regression r limma
5 months ago Jitendra ▴ 10
3
votes
4
replies
557
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
0
votes
10
replies
843
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
6 months ago • updated 11 weeks ago ScafioRuo • 0
10
votes
10
replies
7.4k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 8 weeks ago by • 0 • written 6 months ago by ▴ 10
0
votes
2
replies
582
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
9 months ago • updated 8 months ago yr542 • 0
1
vote
2
replies
635
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
9 months ago Miguel • 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
532
views
Gene enrichment analysis
analysis R GOfuncR
updated 11 months ago by ▴ 730 • written 11 months ago by • 0
0
votes
1
reply
650
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
1
reply
518
views
DEseq2 Single cell data paired design
R
updated 12 months ago by ▴ 30 • written 12 months ago by • 0
0
votes
4
replies
922
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
1
vote
3
replies
888
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
1
vote
2
replies
914
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
0
votes
0
replies
497
views
Are LFQ workflow arguments from DEP package all required or optional?
LFQ R DEP error
13 months ago aymanreffai • 0
0
votes
4
replies
922
views
Unable to install BiocManager
Biocmanager R
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
votes
13
replies
5.0k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
1
vote
1
reply
1.3k
views
Error in h5checktype(). H5Identifier not valid.
rhdf5 rhdf r
updated 13 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
750
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
0
votes
0
replies
481
views
rDGIdb package: score of the results
rDGIdb r
14 months ago HELEN • 0
2
votes
1
reply
529
views
add column with name in R
name R column
updated 14 months ago by ▴ 70 • written 14 months ago by • 0
0
votes
4
replies
891
views
how to extract list in quantile in R
R quantile list
14 months ago sat • 0
0
votes
0
replies
581
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
14 months ago Manav • 0
0
votes
0
replies
577
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics R Bioconducter
14 months ago Jitendra ▴ 10
3
votes
2
replies
828
views
how to extract and match information of two filein R
R column match
14 months ago sat • 0
0
votes
0
replies
527
views
News: Course - R/BIOCONDUCTOR FOR MASS SPECTROMETRY AND PROTEOMICS
Proteomics R Bioconductor MassSpectrometry
14 months ago info ▴ 10
0
votes
17
replies
1.7k
views
How to check linear model
modalmatrix limma R linear
15 months ago • updated 14 months ago Jitendra ▴ 10
0
votes
3
replies
995
views
batch effect in EPIC array data
statistics Epigenetics R
updated 15 months ago by ▴ 730 • written 15 months ago by ▴ 10
0
votes
1
reply
743
views
customised help function in argparse() in R
command-line R command-line-arguments argparse()
updated 15 months ago by 65k • written 15 months ago by • 0
1
vote
2
replies
862
views
Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
15 months ago abhisek001 • 0
0
votes
3
replies
4.0k
views
Reduce the number of nodes appear in the cnetplot of clusterprofiler
cnetplot R clusterProfiler
updated 14 months ago by ★ 4.0k • written 15 months ago by • 0
0
votes
4
replies
983
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2 biomaRt R
15 months ago Dr. • 0
0
votes
1
reply
921
views
Extract Intersection Values from Venn
R Venn
updated 15 months ago by 65k • written 15 months ago by • 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
15 months ago yr542 • 0
0
votes
0
replies
545
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
15 months ago Luomeng • 0
2
votes
9
replies
1.3k
views
mas5calls function doesn't work; mirna40cdf problem
R Bioconductor mas5calls
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
2
replies
1.8k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 15 months ago by 50k • written 16 months ago by • 0
0
votes
3
replies
977
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
657
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 16 months ago by 50k • written 16 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
17 months ago Abdul ▴ 20
0
votes
1
reply
670
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
3
replies
1.1k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 17 months ago by ▴ 150 • written 17 months ago by • 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
1
vote
2
replies
795
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
722
views
ape::dnds produces nan value
R ape dnds nan nanotubes
17 months ago Working • 0
2
votes
4
replies
3.5k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
17 months ago mohammedtoufiq91 ▴ 10
1
vote
7
replies
1.5k
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 17 months ago by 3.9k • written 17 months ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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