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554
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Comment: Comment: Installation error for Rsamtools.
12 months ago ATpoint ★ 5.0k
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2.3k
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Comment: Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
12 months ago ATpoint ★ 5.0k
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2
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2.3k
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Comment: Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
12 months ago ATpoint ★ 5.0k
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2
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1.0k
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Answer: Answer: DESeq2 analysis with transcript counts
12 months ago ATpoint ★ 5.0k
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1
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1.9k
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Answer: Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D
12 months ago ATpoint ★ 5.0k
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1
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788
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Answer: Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
12 months ago ATpoint ★ 5.0k
2
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1.2k
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Answer: Answer: Standardization of rlog transformed counts before PCA
13 months ago ATpoint ★ 5.0k
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0
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1.4k
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Comment: Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
13 months ago ATpoint ★ 5.0k
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1.4k
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Comment: Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
13 months ago ATpoint ★ 5.0k
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1
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1.4k
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Comment: Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
13 months ago ATpoint ★ 5.0k
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0
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3.6k
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Comment: Comment: What type of counts data to import for performing Isoform analysis in edgeR
13 months ago ATpoint ★ 5.0k
2
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1.5k
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Answer: Answer: RSubread output significantly different from bash Subread output
13 months ago ATpoint ★ 5.0k
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1
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3.6k
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Comment: Comment: What type of counts data to import for performing Isoform analysis in edgeR
13 months ago ATpoint ★ 5.0k
1
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1
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3.6k
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Answer: Answer: What type of counts data to import for performing Isoform analysis in edgeR
13 months ago ATpoint ★ 5.0k
0
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0
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782
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Comment: Comment: WGCNA with TPM tables
14 months ago ATpoint ★ 5.0k
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467
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Comment: Comment: eRNAs count
14 months ago ATpoint ★ 5.0k
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556
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Comment: Comment: Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
14 months ago ATpoint ★ 5.0k
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0
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652
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Answer: Answer: DESeq2 rerun returns different results
14 months ago ATpoint ★ 5.0k
1
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0
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1.2k
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Answer: Answer: Handling biological replicates in DESeq2
14 months ago ATpoint ★ 5.0k
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1
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1.7k
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Answer: Answer: Volcano plot has many values around zero
14 months ago ATpoint ★ 5.0k
2
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1
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1.5k
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Comment: Comment: DESeq Input from Salmon + tximport/tximeta
14 months ago ATpoint ★ 5.0k
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0
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1.6k
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Comment: Comment: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
14 months ago ATpoint ★ 5.0k
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0
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787
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Answer: Answer: Average expression of genes across replicates
14 months ago ATpoint ★ 5.0k
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1.0k
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Answer: Answer: Spike-in normalization method in ATACseq
14 months ago ATpoint ★ 5.0k
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0
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2.0k
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Comment: Comment: New to Deseq2 - DEG questions / MA plot
15 months ago ATpoint ★ 5.0k
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1.3k
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Answer: Answer: Analysis of large RNA-Seq Datasets
15 months ago ATpoint ★ 5.0k
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534
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Answer: Answer: how to extract expression matrix post deseq2
15 months ago ATpoint ★ 5.0k
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1.0k
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Answer: Answer: Automatically generate contrasts from a model matrix / formula
15 months ago ATpoint ★ 5.0k
1
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0
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1.4k
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Comment: Comment: Mostly increased counts in differentially accessible peaks using DESeq2
15 months ago ATpoint ★ 5.0k
0
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1
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569
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Answer: Answer: Using Normalized Counts in DESeq2
15 months ago ATpoint ★ 5.0k
0
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1
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1.8k
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Comment: Comment: What should be the normalization protocol for RNA seq data for WGCNA?
15 months ago ATpoint ★ 5.0k
1
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1
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1.8k
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Answer: Answer: What should be the normalization protocol for RNA seq data for WGCNA?
15 months ago ATpoint ★ 5.0k
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1.1k
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Comment: Comment: How to control batch effect if Group and batch are same?
15 months ago ATpoint ★ 5.0k
0
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0
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1.4k
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Comment: Comment: Mostly increased counts in differentially accessible peaks using DESeq2
15 months ago ATpoint ★ 5.0k
5
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1
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1.1k
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Answer: Answer: How to control batch effect if Group and batch are same?
15 months ago ATpoint ★ 5.0k
1
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0
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747
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Comment: Comment: Normalization RNA-seq for multiple plates
15 months ago ATpoint ★ 5.0k
1
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0
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619
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Answer: Answer: DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plo
15 months ago ATpoint ★ 5.0k
0
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1
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2.0k
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Answer: Answer: New to Deseq2 - DEG questions / MA plot
16 months ago ATpoint ★ 5.0k
1
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1
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1.8k
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Comment: Comment: Size factor normalized counts for between sample comparisons - correct?
17 months ago • updated 16 months ago ATpoint ★ 5.0k
1
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1
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1.8k
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Comment: Comment: Size factor normalized counts for between sample comparisons - correct?
17 months ago ATpoint ★ 5.0k
0
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1
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786
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Answer: Answer: Questions in Regards to LFC shrinkage in DSeq2
17 months ago ATpoint ★ 5.0k
1
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0
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883
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Comment: Comment: Gene filtering in DESeq2
17 months ago ATpoint ★ 5.0k
1
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0
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524
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Answer: Answer: Deseq2 - differenc in results
17 months ago ATpoint ★ 5.0k
3
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3
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997
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voom does not seem to properly correct for library size
limma
updated 17 months ago by 53k • written 17 months ago by ★ 5.0k
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0
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997
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Comment: Comment: voom does not seem to properly correct for library size
17 months ago ATpoint ★ 5.0k
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1
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1.2k
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Answer: Answer: More significant genes after lfcShrink in DEseq2?
17 months ago ATpoint ★ 5.0k
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1
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1.6k
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Comment: Comment: RNASeq normlization for samples with global shift in gene expression
17 months ago ATpoint ★ 5.0k
2
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0
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1.8k
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Answer: Answer: DESeq2 is it OK to scale transformed data in order to plot heatmaps?
17 months ago ATpoint ★ 5.0k
2
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1
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934
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Answer: Answer: Why is the inclusion of RUVs not reflected in the EDA plots produced from normal
17 months ago ATpoint ★ 5.0k
0
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0
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1.5k
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Comment: Comment: DiffBind full library size not reliable
17 months ago ATpoint ★ 5.0k
1,105 results • Page 3 of 23
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