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Created An Answer That Has Been Accepted
Awarded 4838 times (see all awards). Earned by the
following contributors:
1 week, 2 days ago
WEHI, Melbourne, Australia
Answer: EdgeR and DESeq2, variance estimation and parametric test
1 week, 4 days ago
WEHI, Melbourne, Australia
Answer: Phenotype effect - building a contrast matrix - grouping vs interaction
2 weeks ago
Wageningen University, Wageningen, the …
Answer: Cluster profiler emap plot - what are the annotations?
4 weeks ago
WEHI, Melbourne, Australia
Answer: Import Salmon data with tximport and pool technical replicates
4 weeks, 1 day ago
United States
Answer: Import Salmon data with tximport and pool technical replicates
1 month ago
Wageningen University, Wageningen, the …
Answer: Broken UNITE 9.0 link (General FASTA Release)
1 month, 1 week ago
WEHI, Melbourne, Australia
Answer: removing the batch effect for vst counts and defining the batches in removeBatch
1 month, 2 weeks ago
Germany
Answer: Zero counts for all samples for all genes downloaded from recount3
1 month, 2 weeks ago
Germany
Answer: DESeq2: full model matrix is less than full rank
1 month, 3 weeks ago
WEHI, Melbourne, Australia
Answer: Adding a group of samples reduces DEGs in other groups
1 month, 3 weeks ago
WEHI, Melbourne, Australia
Answer: loading scores using plotMDS in limma
1 month, 4 weeks ago
WEHI, Melbourne, Australia
Answer: Grouping DEGs yields varying results
1 month, 4 weeks ago
United States
Answer: RNA seq differential expression analysis for large sample size
2 months ago
WEHI, Melbourne, Australia
Answer: Question about RNAseq analysis in EdgeR to identify common and donor specific di
2 months ago
United States
Answer: Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
2 months, 1 week ago
EMBL Heidelberg
Answer: How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.def
2 months, 1 week ago
United States
Answer: Running DEseq2 without "factor" gives unexpected results
2 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: NA p values in edgeR results
2 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: edgeR, RRBS Library size preparation
2 months, 2 weeks ago
United States
Answer: Proper way to implement DESeq2 when comparing samples with trisomies?
2 months, 2 weeks ago
Barcelona/Universitat Pompeu Fabra
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
2 months, 2 weeks ago
Japan
Answer: CAGEr bug report: wrong consensus cluster results
2 months, 2 weeks ago
United States
Answer: Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
2 months, 3 weeks ago
Germany
Answer: Importing RSEM processed data already formatted as a summarized experiment into
2 months, 3 weeks ago
United States
Answer: IsoformSwitchAnalyzeR Error in reading GTF file
3 months ago
WEHI, Melbourne, Australia
Answer: Does this RNAseq experiment require a repeated measures approach?
3 months, 1 week ago
United States
Answer: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
3 months, 2 weeks ago
United States
Answer: P-value histogram of testLinearModel is not uniform
3 months, 3 weeks ago
EMBL Heidelberg
Answer: Use with_go along with other filters in getBM function
3 months, 4 weeks ago
WEHI, Melbourne, Australia
Answer: Extracting fitted expression matrix from Limma
4 months ago
Guangzhou
Answer: Change dotsize to be the same in multiple plots - enrichplot dotplot
4 months ago
Seattle, WA, United States
Answer: SummarizedExperiment is now warning on attach about `read_block` namespace confl
4 months, 2 weeks ago
United States
Answer: Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the
4 months, 2 weeks ago
Cambridge, UK
Answer: Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) :
non-numeric
4 months, 2 weeks ago
WEHI, Melbourne, Australia
Answer: Contrast of Contrasts in Limma
4 months, 3 weeks ago
Seattle, WA, United States
Answer: S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconduct
4 months, 3 weeks ago
United States
Answer: DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
4 months, 4 weeks ago
WEHI, Melbourne, Australia
Answer: edgeR with Successive Differences Contrast Coding?
5 months ago
Cambridge, UK
Answer: how diffbind count the reads of each peak in each sample?
5 months ago
Cambridge, UK
Answer: Positive and negative value fold value in ATAC seq using DiffBind
5 months, 1 week ago
United States
Answer: How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
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