FactoMineR

factoextra — R package for extracting and visualizing multivariate analysis results with ggplot2. Covers PCA (fviz_pca_ind, fviz_pca_var, fviz_pca_biplot), CA (fviz_ca_row, fviz_ca_col, fviz_ca_biplot

1 shared topic • 1 shared operation

Leafcutter — annotation-free RNA splicing quantification from short-read RNA-seq data. Detects differential intron usage, alternative splicing events, outlier splicing (LeafcutterMD), and splicing QTL

1 shared topic • 1 shared operation

Roary — rapid large-scale prokaryotic pan genome analysis. Calculates the pan genome from annotated assemblies (GFF3 from Prokka/Bakta), producing core and accessory gene clusters, gene presence/absen

1 shared topic • 1 shared operation

Use when working with SciPy — the foundational Python scientific computing library — for statistical testing, signal processing, optimization, linear algebra, spatial analysis, and numerical integrati

1 shared topic • 1 shared operation

VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering

1 shared topic • 1 shared operation