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309
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Answer: Answer: Standard QC and EDA for Bulk RNA-seq
5 days ago by i.sudbery 22k
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795
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Comment: Comment: GWAS Manhattan plot shows no SNPs near centromeres — is this result reliable?
7 days ago by i.sudbery 22k
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795
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Comment: Comment: GWAS Manhattan plot shows no SNPs near centromeres — is this result reliable?
7 days ago by i.sudbery 22k
1
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795
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Answer: Answer: GWAS Manhattan plot shows no SNPs near centromeres — is this result reliable?
7 days ago by i.sudbery 22k
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1.5k
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Answer: Answer: Making more complex design in limma removes significant genes
27 days ago by i.sudbery 22k
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1.1k
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Answer: Answer: MOuse Testis Enhancer region
27 days ago by i.sudbery 22k
2
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1
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1.1k
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Answer: Answer: Choosing enrichment analysis tool
4 weeks ago by i.sudbery 22k
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1.0k
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Answer: Answer: Should differential expression analysis be incorporated in cross validation for
4 weeks ago by i.sudbery 22k
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1.1k
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Comment: Comment: Choosing enrichment analysis tool
4 weeks ago by i.sudbery 22k
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3.0k
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Answer: Answer: how to explain the sample size discrepancy in UCSC Xena
7 weeks ago by i.sudbery 22k
12
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4.5k
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Answer: Answer: Linear regression vs DESeq2 models for DEG analysis
7 weeks ago by i.sudbery 22k
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5.5k
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Comment: Comment: Help with Model
7 weeks ago by i.sudbery 22k
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1
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5.5k
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Answer: Answer: Help with Model
7 weeks ago by i.sudbery 22k
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1
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8.4k
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Comment: Comment: miRNA low mapping ratings
7 weeks ago by i.sudbery 22k
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1
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8.4k
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Comment: Comment: miRNA low mapping ratings
7 weeks ago by i.sudbery 22k
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1
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8.4k
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Comment: Comment: miRNA low mapping ratings
7 weeks ago by i.sudbery 22k
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1
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8.4k
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Comment: Comment: miRNA low mapping ratings
7 weeks ago by i.sudbery 22k
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7.6k
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Comment: Comment: RNAseq requirements: Biological and Technical replicates
9 weeks ago by i.sudbery 22k
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9.1k
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Comment: Comment: High percentage of intronic/intergenic reads in RNA-seq
10 weeks ago by i.sudbery 22k
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11k
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Answer: Answer: FDR correction can sometimes lie to you!
3 months ago by i.sudbery 22k
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964
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Comment: Comment: UMI introduction and deduplication with SMARTer-Seq
3 months ago by i.sudbery 22k
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2
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1.6k
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Answer: Answer: Does edgeR supports random effects?
3 months ago by i.sudbery 22k
1
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749
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Comment: Comment: Plotting of genes using tpm matrix
4 months ago by i.sudbery 22k
2
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1
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749
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Comment: Comment: Plotting of genes using tpm matrix
4 months ago by i.sudbery 22k
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536
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Comment: Comment: Identification problem of IDE-8 cell on culture with inverted microscope
4 months ago by i.sudbery 22k
2
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1
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783
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Comment: Comment: Understanding NCBI vs ENA data
4 months ago by i.sudbery 22k
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814
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Comment: Comment: Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be
4 months ago by i.sudbery 22k
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1
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814
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Answer: Answer: Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be
4 months ago by i.sudbery 22k
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0
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928
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Answer: Answer: RNA-seq: TPM batch effect correction
4 months ago by i.sudbery 22k
3
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1.2k
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Comment: Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
4 months ago by i.sudbery 22k
2
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1
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929
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Answer: Answer: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m
updated 4 months ago by 90k • written 4 months ago by 22k
2
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1.2k
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Comment: Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
4 months ago by i.sudbery 22k
0
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0
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771
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Comment: Comment: Should matched samples (not paired) be included in the DESeq2 design model?
5 months ago by i.sudbery 22k
0
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1
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771
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Answer: Answer: Should matched samples (not paired) be included in the DESeq2 design model?
5 months ago by i.sudbery 22k
4
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1
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931
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Answer: Answer: Isoform analysis after quantification with Salmon/Star
5 months ago by i.sudbery 22k
2
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1
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1.1k
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Answer: Answer: pysam header and body
5 months ago by i.sudbery 22k
1
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0
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986
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Comment: Comment: Both up- and down-regulated gene sets return the same GO pathway analysis result
5 months ago by i.sudbery 22k
4
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1
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986
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Answer: Answer: Both up- and down-regulated gene sets return the same GO pathway analysis result
5 months ago by i.sudbery 22k
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1
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2.3k
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Comment: Comment: Trim CDS to ORF
6 months ago by i.sudbery 22k
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1
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2.3k
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Answer: Answer: Trim CDS to ORF
6 months ago by i.sudbery 22k
2
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1
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1.9k
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Comment: Comment: RNASeq bulk transcriptomics analysis
6 months ago by i.sudbery 22k
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0
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197k
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Comment: Comment: Fold change - a final explanation
6 months ago by i.sudbery 22k
1
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1.2k
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Answer: Answer: Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness
6 months ago by i.sudbery 22k
0
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0
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1.2k
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Answer: Answer: miRNA alignment and count generation
6 months ago by i.sudbery 22k
3
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1
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1.5k
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Comment: Comment: Methods for directional pathway analysis of DEGs?
7 months ago by i.sudbery 22k
1
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0
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557
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Answer: Answer: Getting sequences fragments using pysam
7 months ago by i.sudbery 22k
1
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1
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779
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Answer: Answer: MULTIQC for miRNAseq data
7 months ago by i.sudbery 22k
1
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674
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Answer: Answer: Tools for clustering genes rather than samples for bulk RNA-seq
7 months ago by i.sudbery 22k
0
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2.5k
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Comment: Comment: Reproducibility Crisis
7 months ago by i.sudbery 22k
2
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1
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2.5k
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Comment: Comment: Reproducibility Crisis
7 months ago by i.sudbery 22k
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