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Created An Answer That Has Been Accepted
Awarded 5089 times (see all awards). Earned by the
following contributors:
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: Filter genes by expression for voomLmFit
1 year, 9 months ago
United States
Answer: limma::voom vs edgeR::voomLmFit - when to use?
1 year, 9 months ago
Seattle, WA, United States
Answer: DataFrame Printing User Control
1 year, 9 months ago
EMBL Heidelberg
Answer: biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl
1 year, 9 months ago
WEHI, Melbourne, Australia
Answer: Is it appropriate to apply linear mixed models to Voom transformed data?
1 year, 9 months ago
United States
Answer: STRINGdb R package reference class instantiation with v12.0
1 year, 10 months ago
United States
Answer: DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort t
1 year, 10 months ago
United States
Answer: Predicting missing values splines DESeq2
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: limma + voom combine voomWithQualityWeights and duplicateCorrelation
1 year, 10 months ago
Germany
Answer: trying to add SingleR label to Seurat Object fails
1 year, 10 months ago
United States
Answer: DESeq2 unable to handle large count values
1 year, 10 months ago
Cambridge UK
Answer: read10xCounts for Cell Ranger 7 Output
1 year, 10 months ago
Seattle, WA, United States
Answer: Error in Gviz (actually, rtracklayer) | IdeogramTrack
1 year, 10 months ago
WEHI, Melbourne, Australia
Answer: DecideTest vs topTAGs in edgeR
1 year, 10 months ago
United States
Answer: Need help generating BSgenome and orgdb
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: [Bug] Segfault in edgeR::cpm
1 year, 11 months ago
United States
Answer: Subsetting Range Summarized Experiment
1 year, 11 months ago
United States
Answer: Annotation Dbi Error: unable to find an inherited method for function 'x' for si
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsist
1 year, 11 months ago
United States
Answer: SeqSQC R library, functions PCA and IBD not working
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: limma: More differentially expressed genes when factor included in model than wh
1 year, 11 months ago
Cambridge, UK
Answer: DiffBind dba.analyze function doesn't have bSubControl option anymore?
1 year, 11 months ago
United States
Answer: DiffBind returns different grey lists every time I run dba.blacklist even if I s
1 year, 11 months ago
Germany
Answer: ComBat_seq function in sva package does not return a matrix
1 year, 11 months ago
WEHI, Melbourne, Australia
Answer: Batch correction and repeated measures
1 year, 11 months ago
United States
Answer: Remove duplicates of colData in TreeSummarizedExperiment
1 year, 11 months ago
Seattle, WA, United States
Answer: DataFrame Construction With Non-standard Column
2 years ago
WEHI, Melbourne, Australia
Answer: EdgeR and DESeq2, variance estimation and parametric test
2 years ago
WEHI, Melbourne, Australia
Answer: Phenotype effect - building a contrast matrix - grouping vs interaction
2 years ago
Wageningen University, Wageningen, the …
Answer: Cluster profiler emap plot - what are the annotations?
2 years ago
WEHI, Melbourne, Australia
Answer: Import Salmon data with tximport and pool technical replicates
2 years ago
United States
Answer: Import Salmon data with tximport and pool technical replicates
2 years ago
Wageningen University, Wageningen, the …
Answer: Broken UNITE 9.0 link (General FASTA Release)
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: removing the batch effect for vst counts and defining the batches in removeBatch
2 years, 1 month ago
Germany
Answer: Zero counts for all samples for all genes downloaded from recount3
2 years, 1 month ago
Germany
Answer: DESeq2: full model matrix is less than full rank
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Adding a group of samples reduces DEGs in other groups
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: loading scores using plotMDS in limma
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Grouping DEGs yields varying results
2 years, 1 month ago
United States
Answer: RNA seq differential expression analysis for large sample size
2 years, 1 month ago
WEHI, Melbourne, Australia
Answer: Question about RNAseq analysis in EdgeR to identify common and donor specific di
2 years, 1 month ago
United States
Answer: Questions Trying to Re-create MicroArray Data (GSE97562) (Fig. 2)
2 years, 2 months ago
EMBL Heidelberg
Answer: How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.def
2 years, 2 months ago
United States
Answer: Running DEseq2 without "factor" gives unexpected results
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: NA p values in edgeR results
2 years, 2 months ago
WEHI, Melbourne, Australia
Answer: edgeR, RRBS Library size preparation
2 years, 2 months ago
United States
Answer: Proper way to implement DESeq2 when comparing samples with trisomies?
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