6
votes
15
replies
4.3k
views
Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 8.7 years ago by ▴ 150 • written 8.7 years ago by ▴ 280
3
votes
9
replies
5.5k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Bioconductor RNA-seq bed file read-in/download then wavelet transform
bed files wavelet rna-seq
updated 8.7 years ago by 4.2k • written 8.7 years ago by • 0
1
vote
4
replies
2.2k
views
IHW Package for R 3.2.5
deseq2 ihw
8.7 years ago bekah ▴ 40
2
votes
5
replies
2.6k
views
GOseq: count bias correction variations?
Coverage goseq
updated 8.7 years ago by 53k • written 11.4 years ago by ▴ 40
0
votes
6
replies
3.7k
views
Error in lfproc(x, y, weights = weights, cens = cens,... : newsplit: out of vertex space in dba.analyze(diff_contrast, method=DBA_DESEQ2)
atac-seq diffbind
8.7 years ago zhaolin20042008 • 0
1
vote
1
reply
2.0k
views
DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
atac-seq diffbind
8.7 years ago zhaolin20042008 • 0
0
votes
1
reply
2.2k
views
DESeq2 design formula/experiment table help
rnaseq differential gene expression deseq2 r
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
6
votes
5
replies
5.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 20
2
votes
2
replies
5.8k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2 clusterprofiler visualization gseGo
8.7 years ago • updated 5.1 years ago tcalvo ▴ 100
5
votes
4
replies
3.5k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 70
0
votes
1
reply
1.3k
views
tilling sgRNA library design
bioconductor crisprseek
updated 8.7 years ago by ★ 4.3k • written 8.7 years ago by • 0
1
vote
2
replies
1.8k
views
cpgDensityCalc function in Repitools giving contradictory tools
repitools bioconductor cpgDensityCalc
8.7 years ago divyswar01 • 0
0
votes
1
reply
2.0k
views
TF ANALYSIS USING JASPAR
transcription jaspar
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 30
0
votes
3
replies
2.2k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 8.7 years ago by ★ 13k • written 8.7 years ago by • 0
2
votes
2
replies
2.8k
views
Pairwise differential expression analysis with batch effect using edgeR and SVA
edger rna-seq sva differential expression
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
5
votes
2
replies
1.9k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 8.7 years ago by ★ 13k • written 8.7 years ago by • 0
3
votes
7
replies
4.0k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
votes
2
replies
1.9k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
8.7 years ago irizarnaunk • 0
2
votes
6
replies
3.5k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 670
3
votes
2
replies
3.1k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
8.7 years ago shao ▴ 100
3
votes
2
replies
4.4k
views
limma for metabolite data
limma metabolomics limma paired analysis
updated 4.1 years ago by • 0 • written 8.7 years ago by • 0
1
vote
1
reply
4.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.7 years ago stats134711 • 0
0
votes
3
replies
1.6k
views
How to do gene set enrichment analysis on a ranked list of genes expressing leukemia?
bioconductor gcar
8.7 years ago frankchang91 • 0
0
votes
7
replies
4.4k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
8.7 years ago Jeff Skinner • 0
0
votes
1
reply
1.6k
views
oligo rma() function giving unused argument error
oligo rma
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 40
1
vote
3
replies
3.2k
views
DESeq2 Differential Abundance with non-OTU data (e.g. PICRUSt)
deseq2 picrust
8.7 years ago handibles ▴ 20
0
votes
3
replies
1.5k
views
Bimodal p-value histogram for DESeq2 results
deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
votes
2
replies
1.6k
views
What is the confidence interval in ChIPseeker::plotAvgProf?
chipseeker
8.7 years ago enricoferrero ▴ 680
1
vote
10
replies
3.6k
views
Error installing Annaffy
affy annaffy go.db kegg.db
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
votes
0
replies
809
views
The function 'chordDiagramVDJ' from the 'LymphoSeq' Package has 2 code problems
LymphoSeq chordDiagramVDJ
8.7 years ago omran.allatif • 0
0
votes
2
replies
1.4k
views
DiffBind absence of reads
diffbind reads bamfiles
updated 8.7 years ago by ★ 5.2k • written 8.7 years ago by • 0
0
votes
2
replies
1.1k
views
How do I set up the design when I have multiple regions and duplicate timepoints?
limma microarray affy
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
2
votes
4
replies
5.6k
views
What is the best way to subset a DNAStringSet by a GRange ?
bioconductor biostrings granges
updated 8.7 years ago by ★ 11k • written 8.7 years ago by • 0
0
votes
1
reply
1.8k
views
findOverlaps - how to get adjacent ranges?
findOverlaps IRanges
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 20
0
votes
4
replies
2.8k
views
Bioconductor - not updating
bioconductor R bioclite
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
4
votes
6
replies
3.1k
views
mzR (2.8.1) Rcpp (0.12.10) compiler linker issue in Bioconductor 3.4, R 3.3.3
software error mzR Rcpp readMSData2 bioconductor
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
votes
1
reply
1.4k
views
Genomic Ranges package not working
genomicranges assay
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
0
votes
0
replies
831
views
prepareCuff and getCDS functions can not be found when running spliceR
software error
8.7 years ago aura.perez • 0
0
votes
3
replies
2.1k
views
WGCNA crashes R on OSX
WGCNA hclust
8.7 years ago bag59 • 0
0
votes
2
replies
4.6k
views
Calculate correlation matrix for gene expression data
R differential gene expression
updated 8.7 years ago by • 0 • written 8.7 years ago by • 0
2
votes
2
replies
1.4k
views
list fo genes by cnv
cnv genes genomic ranges splitByOverlap
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 30
3
votes
2
replies
1.5k
views
Changing lead developer for existing package
developers bioc-devel
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
0
votes
5
replies
2.3k
views
SomaticSignatures: Transcription Factor Specific Mutation Signature Enrichment
somaticsignatures somaticsignatures package
8.7 years ago morovatunc • 0
0
votes
1
reply
1.3k
views
which contrasts to use? matching contrasts with resultsNames
deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
2
votes
12
replies
3.3k
views
AnnotationHub-cant extract database
annotationhub
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by • 0
2
votes
0
replies
899
views
differential expression with heterogenous disease
heterogenous differential expression individual effects
8.7 years ago aec ▴ 90
0
votes
11
replies
5.5k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 23 months ago by ▴ 230 • written 8.7 years ago by ★ 2.0k
4
votes
20
replies
4.2k
views
TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid for atomic vectors
tcgabiolinks
updated 8.7 years ago by ★ 6.6k • written 8.7 years ago by ▴ 200
3
votes
8
replies
4.2k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2 variancestabilizingtransformation nanostring
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
46,699 results • Page 337 of 934
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Comment: blockwiseModule crashes in the end and doesn't generate modules by gexose2839 • 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA? by TikTsokaasocissalpc • 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. The prob…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
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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