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Created An Answer That Has Been Accepted
Awarded 5053 times (see all awards). Earned by the
following contributors:
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: removing the batch effect for vst counts and defining the batches in removeBatch
1 year, 4 months ago
Germany
Answer: Zero counts for all samples for all genes downloaded from recount3
1 year, 4 months ago
Germany
Answer: DESeq2: full model matrix is less than full rank
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Adding a group of samples reduces DEGs in other groups
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: loading scores using plotMDS in limma
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Grouping DEGs yields varying results
1 year, 4 months ago
United States
Answer: RNA seq differential expression analysis for large sample size
1 year, 4 months ago
WEHI, Melbourne, Australia
Answer: Question about RNAseq analysis in EdgeR to identify common and donor specific di
1 year, 5 months ago
United States
Answer: Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
1 year, 5 months ago
EMBL Heidelberg
Answer: How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.def
1 year, 5 months ago
United States
Answer: Running DEseq2 without "factor" gives unexpected results
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: NA p values in edgeR results
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: edgeR, RRBS Library size preparation
1 year, 5 months ago
United States
Answer: Proper way to implement DESeq2 when comparing samples with trisomies?
1 year, 5 months ago
Barcelona/Universitat Pompeu Fabra
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
1 year, 5 months ago
Japan
Answer: CAGEr bug report: wrong consensus cluster results
1 year, 5 months ago
United States
Answer: Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
1 year, 5 months ago
Germany
Answer: Importing RSEM processed data already formatted as a summarized experiment into
1 year, 5 months ago
United States
Answer: IsoformSwitchAnalyzeR Error in reading GTF file
1 year, 5 months ago
WEHI, Melbourne, Australia
Answer: Does this RNAseq experiment require a repeated measures approach?
1 year, 6 months ago
United States
Answer: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
1 year, 6 months ago
United States
Answer: P-value histogram of testLinearModel is not uniform
1 year, 6 months ago
EMBL Heidelberg
Answer: Use with_go along with other filters in getBM function
1 year, 6 months ago
WEHI, Melbourne, Australia
Answer: Extracting fitted expression matrix from Limma
1 year, 6 months ago
Guangzhou
Answer: Change dotsize to be the same in multiple plots - enrichplot dotplot
1 year, 6 months ago
Miami, US
Answer: TCGAbiolinks cannot find bcr_patient_barcode
1 year, 7 months ago
Seattle, WA, United States
Answer: SummarizedExperiment is now warning on attach about `read_block` namespace confl
1 year, 7 months ago
United States
Answer: Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the
1 year, 7 months ago
Cambridge, UK
Answer: Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) :
non-numeric
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: Contrast of Contrasts in Limma
1 year, 7 months ago
Seattle, WA, United States
Answer: S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconduct
1 year, 7 months ago
United States
Answer: DESeq2 1.40.0 binary install issue on Mac M1 (Bioconductor 3.17)
1 year, 7 months ago
United States
Answer: DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
1 year, 7 months ago
WEHI, Melbourne, Australia
Answer: edgeR with Successive Differences Contrast Coding?
1 year, 8 months ago
Cambridge, UK
Answer: how diffbind count the reads of each peak in each sample?
1 year, 8 months ago
Cambridge, UK
Answer: Positive and negative value fold value in ATAC seq using DiffBind
1 year, 8 months ago
United States
Answer: How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
1 year, 8 months ago
United States
Answer: Using gcrma() and using the t-test to compare single genes of interest for disea
1 year, 8 months ago
United States
Answer: Adding cell population estimates as a covariate in DESeq2 differential gene expr
1 year, 8 months ago
Germany
Answer: Normalisation of data using DESeq2 with multi-groups
1 year, 8 months ago
WEHI, Melbourne, Australia
Answer: Question about transforming log expression values to antilog values in limma
1 year, 8 months ago
United States
Answer: Mistake in Cook's distance calculation in DESeq2 or am I missing something?
1 year, 8 months ago
Italy
Answer: Add 'ColSideColors' using 'heatmap.2' function
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