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Comment: Comment: Obtaining TPM values from STAR alignment and counts with featurecounts using R's
2.4 years ago by Gordon Smyth ★ 8.3k
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3.9k
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Comment: Comment: Obtaining TPM values from STAR alignment and counts with featurecounts using R's
2.4 years ago by Gordon Smyth ★ 8.3k
1
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1
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1.6k
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Comment: Comment: Having problem on doing edgeR anlysis- cant create the DGE list through readbism
2.4 years ago by Gordon Smyth ★ 8.3k
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Answer: Answer: Having problem on doing edgeR anlysis- cant create the DGE list through readbism
2.4 years ago by Gordon Smyth ★ 8.3k
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2.8k
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Answer: Answer: LIMMA: where to find the ANOVA?
2.4 years ago by Gordon Smyth ★ 8.3k
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7.7k
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Comment: Comment: edgeR, Pseudobulk scRNA-seq
2.4 years ago by Gordon Smyth ★ 8.3k
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7.7k
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Answer: Answer: edgeR, Pseudobulk scRNA-seq
2.4 years ago by Gordon Smyth ★ 8.3k
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1.0k
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Answer: Answer: Is it possible to use limma to simultaneously analyze RNA-seq and gene expressio
2.4 years ago by Gordon Smyth ★ 8.3k
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8.0k
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Answer: Answer: What are the advantages of using the T2T as a reference vs GRCh38 today?
2.4 years ago by Gordon Smyth ★ 8.3k
2
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5.1k
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Comment: Comment: Limma: is it necessary to log-transform the data?
2.4 years ago by Gordon Smyth ★ 8.3k
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1
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5.1k
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Comment: Comment: Limma: is it necessary to log-transform the data?
2.4 years ago by Gordon Smyth ★ 8.3k
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5.1k
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Answer: Answer: Limma: is it necessary to log-transform the data?
10 months ago by Gordon Smyth ★ 8.3k
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0
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854
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Answer: Answer: "align" in rsubread only reading 1 out of 6 of my input files
2.4 years ago by Gordon Smyth ★ 8.3k
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2.0k
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Answer: Answer: RNA-seq analysis without replicates
2.4 years ago by Gordon Smyth ★ 8.3k
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1
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1.6k
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Answer: Answer: How to "guess" the transformation based on already-transformed, "normalized coun
2.4 years ago by Gordon Smyth ★ 8.3k
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1.2k
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Answer: Answer: How to Merge RNA Replicates
2.4 years ago by Gordon Smyth ★ 8.3k
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1
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1.4k
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Answer: Answer: suprisingly high logFC using limma
2.4 years ago by Gordon Smyth ★ 8.3k
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1
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2.9k
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Answer: Answer: extract gene coordinates and TSS from gene list
2.5 years ago by Gordon Smyth ★ 8.3k
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1
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2.4k
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Answer: Answer: How to remove unknown batch-batch effects from GEO datasets
2.5 years ago by Gordon Smyth ★ 8.3k
2
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1
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11k
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Comment: Comment: Get TPM from RNA counts and gene length?
2.5 years ago by Gordon Smyth ★ 8.3k
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0
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11k
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Comment: Comment: Get TPM from RNA counts and gene length?
2.5 years ago by Gordon Smyth ★ 8.3k
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0
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3.8k
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Comment: Comment: Limma for batch effect correction
2.5 years ago by Gordon Smyth ★ 8.3k
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1
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11k
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Comment: Comment: Get TPM from RNA counts and gene length?
2.6 years ago by Gordon Smyth ★ 8.3k
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1
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11k
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Comment: Comment: Get TPM from RNA counts and gene length?
2.6 years ago by Gordon Smyth ★ 8.3k
6
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1
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11k
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Answer: Answer: Get TPM from RNA counts and gene length?
2.6 years ago by Gordon Smyth ★ 8.3k
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0
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6.8k
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Comment: Comment: Limma package, how to correct by age and sex?
2.6 years ago by Gordon Smyth ★ 8.3k
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0
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852
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Answer: Answer: How to decide the best threshold for filtering probes in limma
2.6 years ago by Gordon Smyth ★ 8.3k
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0
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944
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Answer: Answer: How should I interpret FB_Plot in microarray analysis?
2.6 years ago by Gordon Smyth ★ 8.3k
3
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1.9k
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Answer: Answer: How should I deduce the variable from its variance and expectation in the `voom`
2.6 years ago by Gordon Smyth ★ 8.3k
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1
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3.8k
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Answer: Answer: Limma for batch effect correction
2.6 years ago by Gordon Smyth ★ 8.3k
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0
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1.3k
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Answer: Answer: interpreting voom mean variance plots with large BCV and faint kink
2.6 years ago by Gordon Smyth ★ 8.3k
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1
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1.1k
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Answer: Answer: finding error to run edgeR, error in ploting MDS and after that in model matrix
2.6 years ago by Gordon Smyth ★ 8.3k
7
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3.8k
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Answer: Answer: Hugely different results between edgeR and DESeq2
2.6 years ago by Gordon Smyth ★ 8.3k
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0
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1.6k
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Answer: Answer: Processed RNA seq data publicly available
2.7 years ago by Gordon Smyth ★ 8.3k
3
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0
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3.9k
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Answer: Answer: R is assigning unique identifier to the same column names when reading in as a d
2.7 years ago by Gordon Smyth ★ 8.3k
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0
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3.2k
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Answer: Answer: R programmin RNA seq
2.7 years ago by Gordon Smyth ★ 8.3k
3
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0
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3.0k
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Comment: Comment: How to make contrasts to find genes DE in one experimental group but NOT in othe
2.7 years ago by Gordon Smyth ★ 8.3k
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0
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998
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Comment: Comment: GSA type of input data
2.7 years ago by Gordon Smyth ★ 8.3k
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2
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3.0k
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Comment: Comment: How to make contrasts to find genes DE in one experimental group but NOT in othe
2.7 years ago by Gordon Smyth ★ 8.3k
4
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1
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3.0k
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Answer: Answer: How to make contrasts to find genes DE in one experimental group but NOT in othe
2.7 years ago by Gordon Smyth ★ 8.3k
2
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0
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1.8k
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Answer: Answer: Strange results from limma output
2.7 years ago by Gordon Smyth ★ 8.3k
1
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1
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2.1k
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Comment: Comment: Accounting for differential abundance in differential expression in scRNAseq
2.8 years ago by Gordon Smyth ★ 8.3k
1
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1
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2.1k
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Answer: Answer: Accounting for differential abundance in differential expression in scRNAseq
2.8 years ago by Gordon Smyth ★ 8.3k
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2.2k
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Comment: Comment: How to remove duplicate rows by averaging their values having 1 million rows X 1
2.8 years ago by Gordon Smyth ★ 8.3k
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1
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2.2k
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Answer: Answer: How to remove duplicate rows by averaging their values having 1 million rows X 1
2.8 years ago by Gordon Smyth ★ 8.3k
5
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1
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4.1k
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Answer: Answer: Different featureCounts data using GTF annotation file from two different source
2.8 years ago by Gordon Smyth ★ 8.3k
1
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0
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747
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Answer: Answer: microarray differential expression analyses
2.8 years ago by Gordon Smyth ★ 8.3k
1
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1
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4.0k
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Comment: Comment: Error input data must be numeric in R, how to solve it?
2.8 years ago by Gordon Smyth ★ 8.3k
2
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1
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4.0k
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Answer: Answer: Error input data must be numeric in R, how to solve it?
2.8 years ago by Gordon Smyth ★ 8.3k
1
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1
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2.6k
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Comment: Comment: Filtering bad quality probes in illumina microarray data
2.8 years ago by Gordon Smyth ★ 8.3k
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