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