53 projects
lightmotif
PyO3 bindings and Python interface to lightmotif, a library for platform-accelerated biological motif scanning using position weight matrices.
scoring-matrices
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
diced
Rust re-implementation of the MinCED algorithm to Detect Instances of CRISPRs in Environmental Data.
pyhmmer
Cython bindings and Python interface to HMMER3.
pymemesuite
Cython bindings and Python interface to the MEME suite.
pyskani
PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
pyjess
Cython bindings and Python interface to JESS, a 3D template matching software.
pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
pytantan
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
pyswrd
Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a heuristic method for fast database search.
pytrimal
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.
mini3di
A NumPy port of the foldseek code for encoding structures to 3di.
pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
pronto
Python frontend to ontologies.
gb-io
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
nafcodec
PyO3 bindings and Python interface to nafcodec, an encoder/decoder for Nucleotide Archive Format (NAF) files.
gecco-tool
Gene cluster prediction with Conditional random fields.
pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
torch-treecrf
A PyTorch implementation of Tree-structured Conditional Random Fields.
fastobo
Faultless AST for Open Biomedical Ontologies in Python.
pyrodigal-gv
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
nmrml2isa
nmrml2isa - nmrML to ISA-Tab parsing tool
fs.sshfs
Pyfilesystem2 over SSH using paramiko
btyper3
In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes
peptides
Physicochemical properties, indices and descriptors for amino-acid sequences.
fs.smbfs
Pyfilesystem2 over SMB using pysmb
sphinxcontrib-svgbob
A Sphinx extension to convert ASCII diagrams to SVGs with Svgbob.
iocursor
A zero-copy file-like wrapper for byte buffers, inspired by Rust's std::io::Cursor.
mzml2isa
mzML file parser and converter to ISA-Tab
rich-msa
A Rich renderable for viewing Multiple Sequence Alignments in the terminal.
fs
Python's filesystem abstraction layer
fs.archive
Enhanced archive filesystems for Pyfilesystem2
moclo
A Python implementation of the MoClo system logic.
orthoani
An implementation of the OrthoANI algorithm for nucleotide identity measurement.
ffpb
A progress bar for ffmpeg. Yay !
instalooter
Another API-less Instagram pictures and videos downloader
nanoset
A memory-optimized wrapper for Python sets likely to be empty.
pyhcrf
A hidden (state) conditional random field (HCRF) implementation written in Python and Cython.
property-cached
A decorator for caching properties in classes (forked from cached-property).
jinja2-fsloader
A Jinja2 template loader using PyFilesystem2
moclo-ecoflex
EcoFlex implementation for the base moclo library.
moclo-ytk
Yeast ToolKit implementation for the base moclo library.
moclo-cidar
CIDAR implementation for the base moclo library.
bindings.rust
A namespace for Python bindings to Rust libraries
bindings.cpp
A namespace for Python bindings to C++ libraries
bindings.c
A namespace for Python bindings to C libraries
bindings
A namespace for Python binding modules
fs.proxy
Miscellaneous proxy filesystems for Pyfilesystem2
dockerasmus
An easy to use docking library.
imzml2isa-qt
A PyQt interface for mzml2isa parser.
mzml2isa-qt
A PyQt interface for mzml2isa parser.
nmrml2isa-qt
A PyQt interface for nmrml2isa parser.