CPTAC Pipelines

Phytozome utilities — search, browse, and download plant genome assemblies, gene annotations, protein sequences, and comparative genomics data from the JGI Phytozome plant genomics portal. Supports qu

3 shared topics • 1 shared operation

ANNOVAR — efficient Perl-based tool for functional annotation of genetic variants from diverse genomes. Supports gene-based, region-based, and filter-based annotation using 100+ databases including Cl

2 shared topics • 2 shared operations

CADD (Combined Annotation Dependent Depletion) -- integrative framework for scoring the deleteriousness of single nucleotide variants and insertion/deletions in the human genome. Combines diverse geno

2 shared topics • 2 shared operations

ComplexHeatmap — R/Bioconductor package for creating highly customizable heatmaps with complex annotations. Supports row/column splitting, multiple annotation tracks (bar, box, point, histogram), Onco

2 shared topics • 2 shared operations

SnpEff — fast Java-based variant annotation and effect prediction tool that annotates genomic variants (SNPs, indels, MNPs) with gene impact, protein changes, loss-of-function predictions, and HGVS no

2 shared topics • 2 shared operations