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3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 14 days ago by • 0 • written 5.2 years ago by • 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
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 4 weeks ago by • 0 • written 7.6 years ago by • 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
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
2
votes
4
replies
3.7k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 9 weeks ago by 50k • written 4.7 years ago by • 0
1
vote
12
replies
2.3k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 12 weeks ago by • 0 • written 2.5 years ago by ▴ 380
0
votes
6
replies
8.6k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 3 months ago by ★ 3.9k • written 7.3 years ago by • 0
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
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.1k • written 6.5 years ago by • 0
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.1 years ago by • 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
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
1
vote
3
replies
1.3k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
22
votes
15
replies
7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
0
votes
2
replies
2.0k
views
Creating a qPCRset object from a text file
qPCRset object nondetects r package txt
updated 6 months ago by • 0 • written 6.3 years ago by • 0
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 6 months ago by • 0 • written 23 months ago by ▴ 40
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 6 months ago by ▴ 40 • written 18 months ago by ▴ 20
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 21 months ago by ▴ 30
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
502
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 10 months ago by • 0 • written 3.2 years 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
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years 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
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 11 months ago by • 0 • written 6.8 years ago by ▴ 10
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
869
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
2
votes
4
replies
1.6k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 12 months ago by • 0 • written 5.4 years ago by • 0
1
vote
4
replies
1.4k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 12 months ago by 50k • written 5.4 years ago by • 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
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
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
3
votes
2
replies
2.1k
views
How to do simple Fisher' exact test for overlapped genomic interval in R?
test fisher exact r findoverlapsofpeaks
updated 12 months ago by • 0 • written 8.3 years ago by ▴ 80
0
votes
3
replies
1.5k
views
How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r bioinformatics peakset
updated 12 months ago by • 0 • written 8.3 years ago by ▴ 80
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
13
replies
4.5k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
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
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
50 results • Page 1 of 1
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Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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
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