The below list is from my scientific experience and perspective. Hope it helps!
Useful omics tools:
- MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis [link]
- Qiita: rapid, web-enabled microbiome meta-analysis [link]
- REVIGO [link] and WEGO [link] for GO annotation and visualization.
- BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud [link]
- MitoMiner 4.0 - A database of mammalian mitochondrial localisation evidence, phenotypes and diseases [link]
- LipiDex: An Integrated Software Package for High-Confidence Lipid Identification [link]
- MetaboList: Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data [link]
Good data handling and analysis packages
- car: Companion to Applied Regression [link]: I sometimes use this package to reassign the name of the columns in the data set.
- forcats for handling categorical variables, especially for visualization [link]. E.g., fct_rev(fct_infreq(x)) for "ordered from top to bottom, highest count to lowest".
- Metabolic profiling series from Springer. Click here for the recent version.
- From mass to metabolite in human untargeted metabolomics: recent advances in annotation of metabolites applying liquid chromatography-mass spectrometry data [link]
- Bad practices in evaluation methodology relevant to class-imbalanced problems [link]