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Comment: Comment: DESEQ2 Results log2fold and pvalue changes after removing genes
3.9 years ago swbarnes2 ★ 1.4k
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Answer: Answer: tximport question on what counts to use for LogFC calculations
4.0 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Troubleshooting DESeq2 Analysis: no DE genes found in subset
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2: Difference between two groups of conditions
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Which rlog should I use for DESeq2 analysis
4.0 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Which interactions terms to choose?
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Complex Contrast in DESeq2
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2 interaction terms in 2x2x2 factorial design
4.0 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Rsamtools : Extracting Unmapped Reads from BAM file
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2 ratio of ratios and p-value
4.0 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't hav
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Batch effect from to sequencing data at differents depths
4.0 years ago swbarnes2 ★ 1.4k
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Answer: Answer: results() function and finding the difference of differences
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2 PlotCounts() function
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: DESeq2 Design Matrix Two Conditions and Two Treatments
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2 Design Matrix Two Conditions and Two Treatments
4.1 years ago swbarnes2 ★ 1.4k
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4.6k
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Comment: Comment: Error connecting to external databases through celldex
4.1 years ago swbarnes2 ★ 1.4k
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4.6k
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Error connecting to external databases through celldex
celldex
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: How to convert TMM RNA-seq file (generated by edgeR) to list of differentially e
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Is it advisable to input a count matrix that consists of reads aligned using dif
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Three conditions and two time points
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: DESeq2 differential expression analysis of protein coding genes only
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Three conditions and two time points
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Three conditions and two time points
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Remove genes in a list from cts
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Three conditions and two time points
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Remove genes in a list from cts
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Question on the fold change estimate
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: scRNAseq analysis on multiple datasets
4.1 years ago swbarnes2 ★ 1.4k
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Answer: Answer: DESeq2: All samples have 0 counts for all genes. check the counting script
4.1 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Interpretation of DESeq2 results with 3 factorial design with interaction terms.
4.1 years ago swbarnes2 ★ 1.4k
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2.6k
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Answer: Answer: Interpretation of DESeq2 results with 3 factorial design with interaction terms.
4.1 years ago swbarnes2 ★ 1.4k
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1.9k
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Comment: Comment: Understanding output of Negative Binomial in DESeq2
4.2 years ago swbarnes2 ★ 1.4k
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924
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Answer: Answer: Log fold change interpretation of time series with Wald test
4.2 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Sequencing depth before and aftr normalisation with DESEQ2 doesn't look as expec
4.2 years ago swbarnes2 ★ 1.4k
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7.7k
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Comment: Comment: How does edgeR calculate fold change?
4.2 years ago swbarnes2 ★ 1.4k
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7.7k
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Answer: Answer: How does edgeR calculate fold change?
4.2 years ago swbarnes2 ★ 1.4k
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Comment: Comment: normalising Biological replicates for differential analysis
4.2 years ago swbarnes2 ★ 1.4k
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961
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Comment: Comment: normalising Biological replicates for differential analysis
4.2 years ago swbarnes2 ★ 1.4k
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Comment: Comment: DESEQ PCA
4.2 years ago swbarnes2 ★ 1.4k
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Comment: Comment: DESEQ PCA
4.2 years ago swbarnes2 ★ 1.4k
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Answer: Answer: Error in curl; timeout when using biomaRt
4.2 years ago swbarnes2 ★ 1.4k
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Comment: Comment: DeSeq2_ result different _3 factor level Deseq2 vs 2 factor level Deseq2
4.2 years ago swbarnes2 ★ 1.4k
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Comment: Comment: Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
4.3 years ago swbarnes2 ★ 1.4k
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3.6k
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Comment: Comment: Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
4.3 years ago swbarnes2 ★ 1.4k
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2.3k
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Comment: Comment: Differential Expression analysis of specific list of genes
4.3 years ago swbarnes2 ★ 1.4k
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2.3k
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Answer: Answer: Differential Expression analysis of specific list of genes
4.3 years ago swbarnes2 ★ 1.4k
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1.9k
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Answer: Answer: Deseq paired samples
4.3 years ago swbarnes2 ★ 1.4k
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9.3k
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Comment: Comment: package to manipulate GTF files
4.3 years ago swbarnes2 ★ 1.4k
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1
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9.3k
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Comment: Comment: package to manipulate GTF files
4.3 years ago swbarnes2 ★ 1.4k
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