Science::Bioinformatics

Fast TUI toolkit for viewing, translating, and manipulating biological sequences.

fuzzyfold's secondary structure representations.

fuzzyfold's stochastic secondary structure simulations.

fuzzyfold's nearest neighbor free energy evaluations.

Nucleic acid secondary structure kinetics.

Ultra high-throughput processing of 10x-flex single-cell sequencing data

Helpful functions to handle PDB files

A library to draw mass spectra

A high efficiency binary format for sequencing data

Rust bindings for the digest library

Automatically generated FFI definitions for abPOA

Rust bindings for abPOA: Adaptive Banded POA

An implementation of the SAIS algorithm for suffix array construction

Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags.

Simple bioinformatics CLI tools for sequence analysis and manipulation

Generate restraints to be used in HADDOCK

Counter-attack nonhuman bad actors that abuse Frequency-shift Keying and Phase-shift Keying in your human environment thusly soothing your temporal and occipital lobes.

The Bismark bisulfite-sequencing suite (Rust) — the bismark aligner, deduplicate_bismark, bismark_methylation_extractor, bismark2bedGraph, coverage2cytosine, bismark_genome_preparation, bam2nuc, NOMe_filtering, filter_non_conversion, methylation_consistency, bismark2report, bismark2summary, all in one crate.

Library for creating FM-indexes from FASTA/FASTQ files. AWRY is able to search at lightning speed by leveraging SIMD vectorization and multithreading over collections of queries.

FFI library for the NCBI VDB

A SIMD-accelerated library to compute a b-bit bottom-h sketch

Microbiology friendly bioinformatics Rust functions

FASTA-to-JSON CLI wrapper for Immunum antibody sequence numbering

Microbiology friendly bioinformatics Rust functions

Rust port of Bismark Perl's filter_non_conversion script

Platform-Accelerated Package for Alignment-free SMURF analysis.

PyO3 bindings and Python interface to PAPASMURF, a Platform-Accelerated Package for Alignment-free SMURF analysis.

Shared deterministic SIMD primitives for Kira tools.

PlasCAD

ggetrs submodule for querying BLAST

ggetrs submodule for querying ENSEMBL

ggetrs submodule for querying archs4

ggetrs submodule for querying ENRICHR

ggetrs submodule for querying CHEMBL

This is a sequence processing tool written in Rust for manipulating FASTA/FASTQ files. Pure rust version of seqtk.

My sequences please - a paired fastq grepper with regex support

ggetrs submodule for querying STRING

ggetrs submodule for querying NCBI

ggetrs submodule for querying PDB

ggetrs submodule for querying UCSC

ggetrs submodule for querying UNIPROT

Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations.

A minimal, zero-copy streaming parser for FASTA/FASTQ files

Rust port of Bismark Perl's bismark2report script (per-sample graphical HTML report)

Bismark-aware BAM/SAM/CRAM I/O on top of noodles

Rust port of the Bismark Perl aligner wrapper (bismark)

Rust port of Bismark Perl's bismark2bedGraph script

Rust port of Bismark Perl's coverage2cytosine script (Phase A: scaffold + CLI + genome reader)

Rust port of Bismark Perl's deduplicate_bismark script

Rust port of Bismark Perl's bam2nuc script (mono-/di-nucleotide coverage QC)