MatrixEQTL

Use when working with data.table — the high-performance R package for fast data manipulation, aggregation, and file I/O on large datasets. data.table extends data.frame with a concise DT[i, j, by] syn

3 shared topics

bamutil — C++ toolkit for reading, writing, and manipulating BAM alignment files. Provides duplicate marking (dedup), base quality score recalibration (recab), overlapping read clipping (clipOverlap),

2 shared topics • 1 shared operation

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

MAFFT — multiple sequence alignment for nucleotide and protein sequences. Implements progressive (FFT-NS-1, FFT-NS-2), iterative refinement (FFT-NS-i), and consistency-based iterative methods (L-INS-i

2 shared topics • 1 shared operation

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

2 shared topics • 1 shared operation