Table 1 Software used for the analysis
From: Multi-omics analysis of functional substances and expression verification in cashmere fineness
Analytical projects | Omics | Software |
|---|---|---|
Comparison analysis | Transcriptomics | Hisat2 (2.0.5) |
Translatomics | Tophat2 (2.0.12) | |
Bowtie (1.0.1) | ||
Quantitative analysis | Transcriptomics | FeatureCounts (1.5.0-p3) |
Stringtie (1.3.3b) | ||
Translatomics | FeatureCounts (1.5.0-p3) | |
HTseq (v0.6.1) | ||
Proteomics | Proteome Discoverer (2.2) | |
Metabolomics | Compound Discoverer (2.2) | |
Difference analysis | Transcriptomics | DESeq2 (1.16.1) |
EdgeR (3.18.1) | ||
Translatomics | DESeq2 (1.14.1) | |
EdgeR (3.16.4) | ||
Proteomics | R (3.4.3) | |
Metabolomics | R (3.4.3) | |
Differential TE gene analysis | Multi-omics | RiboDiff (V.0.2.1) |
Xtail (1.1.5) | ||
Enrichment analysis | Multi-omics | ClusterProfiler (3.4.4) |