Phytozome

CPTAC pipelines — Python toolkit for accessing and analyzing Clinical Proteomic Tumor Analysis Consortium (CPTAC) multi-omics cancer data. Provides programmatic download of proteomics, phosphoproteomi

3 shared topics • 1 shared operation

Use when working with the Arrow R package in genomics, transcriptomics, proteomics, or other R/Bioconductor-adjacent pipelines that need Parquet, Feather/IPC, CSV, JSON, or larger-than-memory datasets

3 shared topics

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

2 shared topics • 1 shared operation

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

2 shared topics • 1 shared operation

Pyrodigal is a Python library binding to Prodigal for gene prediction in prokaryotic genomes and metagenomes. Provides in-memory ORF finding with SIMD-accelerated scoring, single-genome and metagenomi

2 shared topics • 1 shared operation