0
votes
1
reply
800
views
NA value in padj but only for certain contrasts
DESeq2
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 10
1
vote
12
replies
3.9k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 670
0
votes
1
reply
759
views
DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
1.4k
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 3.2 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
1
reply
930
views
Design structure
DESeq2 des
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
1
vote
2
replies
1.3k
views
Question about contrasts in DESeq2
DESeq2
3.2 years ago • updated 3.1 years ago marinaw ▴ 20
0
votes
1
reply
1.2k
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
0
votes
1
reply
889
views
Strange dispersion plot with high outliers
DESeq2
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
0
votes
1
reply
1000
views
How to extract DeSeq2 results for the different groups?
DESeq2
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
0
votes
1
reply
860
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
0
replies
1.0k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
vote
3
replies
1.2k
views
Older source of biocFileCache package
biomaRt
updated 3.1 years ago by ★ 6.6k • written 3.1 years ago by • 0
1
vote
3
replies
1.8k
views
Problem with DESeq2
DESeq2 apple-m1
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
votes
1
reply
911
views
Empty ChipQC Report
ChipQCReport
updated 3.0 years ago by • 0 • written 3.1 years ago by • 0
1
vote
3
replies
1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
1
reply
3.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
2
replies
1.5k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
3.1 years ago stacy.genovese • 0
0
votes
4
replies
1.5k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.1 years ago by • 0
0
votes
3
replies
1.6k
views
Difficulty creating summarized experiment
sesame sesameData
updated 3.1 years ago by ▴ 20 • written 3.1 years ago by • 0
0
votes
2
replies
1.3k
views
Error received in ropls package
Metabolomics ropls
updated 3.1 years ago by ▴ 40 • written 3.1 years ago by • 0
1
vote
3
replies
7.6k
views
Not able to install packages in Bioconductor version '3.16'
Install BiocManager version3.16
updated 3.0 years ago by 4.3k • written 3.1 years ago by • 0
1
vote
5
replies
1.6k
views
how can I add a label for granges using the geom_rect ?
ggbio
3.1 years ago 潘晓光 • 0
0
votes
1
reply
1.8k
views
DESeq2 design function and downstream analyses
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
6
votes
6
replies
2.3k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
3.1 years ago Sara ▴ 20
0
votes
2
replies
1.3k
views
Filtering normalised counts
DESeq2
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
1
reply
2.7k
views
Instaling glmGamPoi
glmGamPoi
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
1
vote
1
reply
1.1k
views
ggcyto::scale_x_logicle() not converging
ggcyto
updated 3.1 years ago by 4.3k • written 3.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
2
replies
2.5k
views
object of type 'externalptr' is not subsettable in R4.0 - with COM Object
r4.0 ComponentObjectModel subsetting
3.2 years ago • updated 3.1 years ago Duy Duc • 0
0
votes
0
replies
989
views
Job: Post Doctoral Research Officer - Bioinformatics
JobPosting
3.1 years ago hdawson • 0
2
votes
3
replies
3.1k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 3.0 years ago by • 0 • written 3.1 years ago by ▴ 10
0
votes
1
reply
1.5k
views
How to remove INDELS/SNPs from a bed file
SNP
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
1.5k
views
WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
3.1 years ago • updated 15 months ago bioinformaticssrm2011 • 0
1
vote
1
reply
927
views
add genome to BSgenome
bsgenome
updated 3.1 years ago by 4.3k • written 3.1 years ago by ▴ 10
3
votes
6
replies
2.2k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.1 years ago by • 0
0
votes
0
replies
1.2k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
3.1 years ago gogniu • 0
2
votes
5
replies
1.7k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR RNAseq123
updated 3.1 years ago by 53k • written 3.1 years ago by ▴ 50
0
votes
1
reply
544
views
DESeq2 effect of interaction when using a grouping variable
DESeq2
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
2
votes
8
replies
2.9k
views
error in getting entrez ids for gene names
Bioconductor
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
3
votes
3
replies
1.4k
views
Subset and Assign MultiAssayExperiment
MultiAssayExperiment
updated 3.1 years ago by 700 • written 3.1 years ago by ★ 1.6k
4
votes
3
replies
2.0k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
0
votes
2
replies
1.4k
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
3.1 years ago Sally • 0
0
votes
0
replies
1.3k
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
cancer bioinformatics proteomics genomics phd
3.1 years ago DKFZ International PhD Program ▴ 10
0
votes
0
replies
1.0k
views
Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
3.1 years ago Rom • 0
0
votes
1
reply
1.1k
views
empty values when extracting beta values using the GEOquery
GSE61380 GEOquery
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
1
vote
4
replies
1.2k
views
DESeq2 says my sampleinfo has linear combination error but I don't see it...
DESeq2
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
votes
2
replies
1.7k
views
Error loading package MSnbase on MacOS
MSnbase
updated 3.1 years ago by 1.6k • written 3.1 years ago by • 0
1
vote
2
replies
1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.1 years ago mohammedtoufiq91 ▴ 10
0
votes
4
replies
1.4k
views
Time course experiment with limma voom
limma
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
46,712 results • Page 70 of 935
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Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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