Showing : r • reset
1
vote
1
reply
828
views
roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
0
votes
2
replies
1.2k
views
R Bioconductor package Affxparser keeps crashing
affxparser r Bioconductor
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
9
votes
3
replies
9.6k
views
Limma vs deseq2 results
limma RNASeq R
3.5 years ago k___ ▴ 30
2
votes
3
replies
3.0k
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 30
1
vote
1
reply
1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
3
votes
3
replies
2.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
0
votes
6
replies
2.0k
views
regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
3.5 years ago Jitendra ▴ 10
4
votes
6
replies
2.3k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3.6 years ago • updated 3.5 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
2.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3.6 years ago • updated 3.5 years ago takemoto • 0
1
vote
1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.5 years ago by 53k • written 3.6 years ago by • 0
0
votes
1
reply
1.2k
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
1
reply
1.8k
views
trouble installing DESeq2
install packages R DESeq2
updated 3.6 years ago by 4.2k • written 3.6 years ago by • 0
0
votes
3
replies
4.8k
views
Problem with gcc/fortran compilers in new version of Bioconductor (Mac M1)
biocmanager R gofortran Bioconductor
3.6 years ago Olivia • 0
8
votes
5
replies
11k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 12 months ago by • 0 • written 3.6 years ago by ▴ 50
5
votes
14
replies
7.4k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.6 years ago by ★ 5.0k • written 7.4 years ago by ▴ 60
0
votes
11
replies
3.1k
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData r
3.6 years ago Mohamed ▴ 30
1
vote
3
replies
2.9k
views
GVIZ giving error with loading hg38 genome
R Gviz
3.6 years ago RUser743 • 0
0
votes
7
replies
2.0k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
3.6 years ago JAcky • 0
2
votes
1
reply
1.3k
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by • 0
1
vote
5
replies
3.8k
views
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
clusterProfiler r
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
22
votes
15
replies
12k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 2.1 years ago by ▴ 10 • written 3.7 years ago by ▴ 50
0
votes
3
replies
1.8k
views
lfcShrink contrast
lfcshrink R DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology
clinical R bioinformatics multiomics oncology
3.7 years ago vincent.piras • 0
0
votes
1
reply
3.3k
views
How can i download maf files form GDC Data Portal?
maf R
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
2
votes
3
replies
3.0k
views
Ensembl non responsive
ensembl R
3.7 years ago ksci ▴ 20
0
votes
2
replies
2.8k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
3.7 years ago • updated 3.2 years ago spyrouglykeria • 0
3
votes
2
replies
1.8k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.7 years ago • updated 3.6 years ago Dakarai ▴ 10
0
votes
2
replies
6.1k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.7 years ago by ▴ 20 • written 3.7 years ago by • 0
0
votes
1
reply
933
views
Error running hierClust
hierClust R SNPs clustering
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
0
replies
884
views
normalisation options in RnBeads
Epigenetics RnBeads R Bioconducter
3.7 years ago Jitendra ▴ 10
4
votes
8
replies
4.2k
views
R package installation error
HPC R Bioconducter
3.7 years ago Jitendra ▴ 10
0
votes
0
replies
2.1k
views
How to pool phyloseq data?
phyloseq r
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
3
replies
1.9k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
4
votes
4
replies
1.3k
views
motifStack Plotting the correct data positions on x axis
motifStack R
3.7 years ago Marwah • 0
0
votes
8
replies
2.8k
views
error in RnBeads installation
Epigenetics RnBeads R
3.7 years ago Jitendra ▴ 10
0
votes
2
replies
3.4k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
3.8 years ago nakane_clan • 0
0
votes
1
reply
1.6k
views
Running limma in parallel
parallel R limma EWAS
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
2
votes
2
replies
2.0k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.8 years ago Hasan Alanya • 0
0
votes
0
replies
707
views
Error in DEqMS proteomics analysis
DEqMS R DifferentialExpression
3.8 years ago Mrinal.singh06 • 0
0
votes
0
replies
1.1k
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.8 years ago Lorenzo • 0
2
votes
3
replies
5.9k
views
fgsea not downloading due to new r version. Is there a way around this?
r fgsea
3.9 years ago amir.khan • 0
0
votes
0
replies
852
views
RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
0
votes
3
replies
2.2k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.8 years ago by 21k • written 3.9 years ago by ▴ 10
1
vote
3
replies
2.4k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
7
replies
2.1k
views
Centos 7.8, custom-compiled R-4.1: iPath_1.0.0 won't install
error iPath R compilation
3.9 years ago wjb2130 • 0
0
votes
0
replies
1.1k
views
DBA Error in DiffBind - How to format sampleSheet
DBA R DifferentialPeakCalling
4.0 years ago opheevallee • 0
0
votes
1
reply
2.0k
views
values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
0
votes
0
replies
1.3k
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
4.0 years ago Paulina • 0
0
votes
0
replies
1.4k
views
RCurl installation failure
R
4.1 years ago conbward • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology
bioinformatics omics R oncology France
4.1 years ago vincent.piras • 0
1,163 results • Page 3 of 24
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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