Showing : R • reset
1
vote
1
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788
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roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
votes
2
replies
1.2k
views
R Bioconductor package Affxparser keeps crashing
affxparser r Bioconductor
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
9
votes
3
replies
9.5k
views
Limma vs deseq2 results
limma RNASeq R
3.4 years ago k___ ▴ 30
2
votes
3
replies
2.9k
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 3.4 years ago by 53k • written 3.4 years ago by ▴ 30
1
vote
1
reply
1.3k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
3
votes
3
replies
2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
0
votes
6
replies
2.0k
views
regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
3.4 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
3.4 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
2.5k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3.4 years ago takemoto • 0
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
0
votes
1
reply
1.2k
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
1
reply
1.7k
views
trouble installing DESeq2
install packages R DESeq2
updated 3.4 years ago by 4.2k • written 3.4 years ago by • 0
0
votes
3
replies
4.7k
views
Problem with gcc/fortran compilers in new version of Bioconductor (Mac M1)
biocmanager R gofortran Bioconductor
3.4 years ago Olivia • 0
8
votes
5
replies
11k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 10 months ago by • 0 • written 3.4 years ago by ▴ 50
5
votes
14
replies
7.3k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.4 years ago by ★ 5.0k • written 7.3 years ago by ▴ 60
0
votes
11
replies
3.0k
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData r
3.5 years ago • updated 3.4 years ago Mohamed ▴ 30
1
vote
3
replies
2.8k
views
GVIZ giving error with loading hg38 genome
R Gviz
3.5 years ago RUser743 • 0
0
votes
7
replies
1.9k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
3.5 years ago • updated 3.4 years ago JAcky • 0
2
votes
1
reply
1.2k
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3.5 years ago by ▴ 100 • written 3.5 years ago by • 0
1
vote
5
replies
3.7k
views
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
clusterProfiler r
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
22
votes
15
replies
11k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 23 months ago by ▴ 10 • written 3.5 years ago by ▴ 50
0
votes
3
replies
1.7k
views
lfcShrink contrast
lfcshrink R DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 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
3.5 years ago vincent.piras • 0
0
votes
1
reply
3.2k
views
How can i download maf files form GDC Data Portal?
maf R
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
2
votes
3
replies
2.9k
views
Ensembl non responsive
ensembl R
3.5 years ago ksci ▴ 20
0
votes
2
replies
2.8k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
3.5 years ago • updated 3.0 years ago spyrouglykeria • 0
3
votes
2
replies
1.7k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.5 years ago • updated 3.4 years ago Dakarai ▴ 10
0
votes
2
replies
5.9k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.5 years ago by ▴ 20 • written 3.6 years ago by • 0
0
votes
1
reply
906
views
Error running hierClust
hierClust R SNPs clustering
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
votes
0
replies
859
views
normalisation options in RnBeads
Epigenetics RnBeads R Bioconducter
3.5 years ago Jitendra ▴ 10
4
votes
8
replies
4.1k
views
R package installation error
HPC R Bioconducter
3.6 years ago Jitendra ▴ 10
0
votes
0
replies
2.0k
views
How to pool phyloseq data?
phyloseq r
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
vote
3
replies
1.8k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
4
votes
4
replies
1.3k
views
motifStack Plotting the correct data positions on x axis
motifStack R
3.6 years ago Marwah • 0
0
votes
8
replies
2.7k
views
error in RnBeads installation
Epigenetics RnBeads R
3.6 years ago Jitendra ▴ 10
0
votes
2
replies
3.4k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
3.6 years ago nakane_clan • 0
0
votes
1
reply
1.5k
views
Running limma in parallel
parallel R limma EWAS
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
2
votes
2
replies
1.9k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.7 years ago Hasan Alanya • 0
0
votes
0
replies
676
views
Error in DEqMS proteomics analysis
DEqMS R DifferentialExpression
3.7 years ago Mrinal.singh06 • 0
0
votes
0
replies
1.1k
views
WGCNA with large Methylation matrix
wgcna R WGCNA Methylation
3.7 years ago Lorenzo • 0
2
votes
3
replies
5.8k
views
fgsea not downloading due to new r version. Is there a way around this?
r fgsea
3.7 years ago amir.khan • 0
0
votes
0
replies
823
views
RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 3.7 years ago by 21k • written 3.7 years ago by • 0
0
votes
3
replies
2.1k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 3.6 years ago by 21k • written 3.7 years ago by ▴ 10
1
vote
3
replies
2.3k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.7 years ago by 43k • written 3.8 years ago by • 0
0
votes
7
replies
2.0k
views
Centos 7.8, custom-compiled R-4.1: iPath_1.0.0 won't install
error iPath R compilation
3.8 years ago • updated 3.7 years ago wjb2130 • 0
0
votes
0
replies
1.1k
views
DBA Error in DiffBind - How to format sampleSheet
DBA R DifferentialPeakCalling
3.9 years ago opheevallee • 0
0
votes
1
reply
1.9k
views
values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by • 0
0
votes
0
replies
1.2k
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
3.9 years ago Paulina • 0
0
votes
0
replies
1.3k
views
RCurl installation failure
R
3.9 years ago conbward • 0
0
votes
0
replies
1.2k
views
Job: Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology
bioinformatics omics R oncology France
3.9 years ago vincent.piras • 0
1,163 results • Page 3 of 24
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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