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Answer: Answer: How can i fix this problem in R
22 months ago Steve Lianoglou ★ 13k
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2
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1.9k
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Answer: Answer: Help with limma contrast, difference of a difference?
22 months ago Steve Lianoglou ★ 13k
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1
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1.1k
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Answer: Answer: multiple annotated 3'UTR for same transcript from bioMart
23 months ago Steve Lianoglou ★ 13k
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1
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1.9k
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Answer: Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
23 months ago Steve Lianoglou ★ 13k
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1
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1.8k
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Answer: Answer: unbalanced cell count and unbalanced read count across samples in pseudobulk dif
2.0 years ago Steve Lianoglou ★ 13k
1
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1
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844
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Answer: Answer: I want to clarify difference between below two codes for analysis of DEGs. I got
2.0 years ago Steve Lianoglou ★ 13k
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2.8k
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Answer: Answer: TPM to raw counts
2.3 years ago Steve Lianoglou ★ 13k
1
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0
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643
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Answer: Answer: limma KNN classification with voom-transformed data
2.4 years ago Steve Lianoglou ★ 13k
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1
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1.7k
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Answer: Answer: DEseq2 replicate normalization
2.4 years ago Steve Lianoglou ★ 13k
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1
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1.3k
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Answer: Answer: edgeR shows different results for same dataset
2.4 years ago Steve Lianoglou ★ 13k
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1
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948
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Answer: Answer: Identifying presence of certain genes
2.5 years ago Steve Lianoglou ★ 13k
0
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685
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Answer: Answer: Pushing a new build of package to Bioconductor
2.7 years ago Steve Lianoglou ★ 13k
2
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1.2k
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Answer: Answer: No counts, just fold change data
2.9 years ago Steve Lianoglou ★ 13k
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1
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2.1k
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Answer: Answer: CibersortX running error for Single cell-RNA
2.9 years ago Steve Lianoglou ★ 13k
1
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1
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2.3k
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Answer: Answer: scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
3.3 years ago Steve Lianoglou ★ 13k
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1.4k
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Answer: Answer: Treatment AND Sex in EdgeR
3.4 years ago Steve Lianoglou ★ 13k
5
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1
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908
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Answer: A: edgeR and batch effects
3.6 years ago Steve Lianoglou ★ 13k
4
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1.5k
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Answer: A: Calculating standard deviation for a few genes using RNAseq data
3.6 years ago Steve Lianoglou ★ 13k
0
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0
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6.0k
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Answer: A: scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
3.7 years ago Steve Lianoglou ★ 13k
1
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0
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705
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Answer: A: treating RNA-seq gene expression data in cpm for edgeR
4.0 years ago Steve Lianoglou ★ 13k
1
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1
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3.2k
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Answer: A: Possible batch effect correction with RNA-Seq data when the batches do not conta
4.0 years ago Steve Lianoglou ★ 13k
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0
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705
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Answer: A: RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly diff
4.1 years ago Steve Lianoglou ★ 13k
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1
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884
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Answer: A: Any possibility to "cache" TxDb object?
4.2 years ago Steve Lianoglou ★ 13k
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0
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18k
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Answer: A: R studio input style for generating heatmap (RNAseq)
4.2 years ago Steve Lianoglou ★ 13k
2
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2
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1.2k
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Answer: A: Design to analyze experiment with multiple samples from the same biological enti
4.2 years ago Steve Lianoglou ★ 13k
1
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0
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468
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Answer: A: limma how to extract rest of output
4.2 years ago Steve Lianoglou ★ 13k
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1
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749
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Answer: A: DESeq2 Complex Model
4.2 years ago Steve Lianoglou ★ 13k
0
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0
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13k
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Answer: A: Update all/some/none? [a/s/n]:
4.2 years ago Steve Lianoglou ★ 13k
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0
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1000
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Answer: A: I have installed bioconductor, R still asks me to install it
4.3 years ago Steve Lianoglou ★ 13k
1
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1
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1.6k
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Answer: A: Error with cell annotation using singleR
4.3 years ago Steve Lianoglou ★ 13k
1
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1
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802
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Answer: A: Should the rlog normalised gene expression counts be further normalised?
4.4 years ago Steve Lianoglou ★ 13k
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0
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1.1k
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Answer: A: PureCN version clashes at GitHub and Bioconductor
4.4 years ago Steve Lianoglou ★ 13k
3
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0
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1.5k
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Answer: A: Limma analysis on a subset of data
4.5 years ago Steve Lianoglou ★ 13k
3
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2
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1.8k
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Answer: A: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
4.6 years ago Steve Lianoglou ★ 13k
0
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0
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1.4k
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Answer: A: Subsetting a data frame generated by topTable() {limma}
4.6 years ago Steve Lianoglou ★ 13k
1
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1
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3.3k
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Answer: A: Limma residuals matrix
4.7 years ago Steve Lianoglou ★ 13k
1
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1
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2.0k
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Answer: A: How can I delete specific rows (using gene name) from a DESeq2 dataset (or even
4.7 years ago Steve Lianoglou ★ 13k
3
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1
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1.8k
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Answer: A: RNA-seq normalization without filtering
4.7 years ago Steve Lianoglou ★ 13k
5
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0
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8.1k
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Answer: A: What can I do if I only have TPM but not raw counts data?
4.8 years ago Steve Lianoglou ★ 13k
1
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2
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1.5k
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Answer: A: "Packages required but not available." rtracklayer in OSX is not available to CR
4.8 years ago Steve Lianoglou ★ 13k
0
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2
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1.8k
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Answer: A: Comparing two different sequencing method by DEseq2
4.8 years ago Steve Lianoglou ★ 13k
1
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1
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6.2k
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Answer: A: DESeq2 GLM modelling and Wald's test
4.9 years ago Steve Lianoglou ★ 13k
0
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0
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603
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Answer: A: Using already normalized counts
4.9 years ago Steve Lianoglou ★ 13k
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1
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1.1k
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Answer: A: Bioconductor support site search missing results?
4.9 years ago Steve Lianoglou ★ 13k
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0
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1.2k
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Answer: A: TCGA isoform expression quantification file - how to reshape data
4.9 years ago Steve Lianoglou ★ 13k
0
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1
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1.1k
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Answer: A: Number and percent of mapped reads from RNA seq analysis.
5.1 years ago Steve Lianoglou ★ 13k
1
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1
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2.7k
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Answer: A: Use of pseudoalignment estimated counmts as input to edgeR and Limma-Voom
5.2 years ago Steve Lianoglou ★ 13k
0
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1
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2.9k
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Answer: A: scRNA-seq: a question about the names of the columns in a Seurat object
5.4 years ago Steve Lianoglou ★ 13k
2
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0
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966
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Answer: A: Help for Research Proposal
5.4 years ago Steve Lianoglou ★ 13k
0
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1
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1.0k
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Answer: A: Get normalized COUNTS Deseq2
5.4 years ago Steve Lianoglou ★ 13k
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