66 projects
pyncbitk-runtime
Runtime component of the NCBI C++ Toolkit to use in PyNCBItk.
pyinfernal
Cython bindings and Python interface to Infernal.
chamois-tool
Chemical HierArchy for Metabolites Obtained In Silico.
gecco
Gene Cluster prediction with Conditional random fields.
pyhmmer
Cython bindings and Python interface to HMMER3.
scoring-matrices
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
pronto
Python frontend to ontologies.
pyaragorn
Cython bindings and Python interface to ARAGORN, a tRNA and mtRNA detection software.
pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
pyjess
Cython bindings and Python interface to JESS, a 3D template matching software.
pytrimal
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.
pyabricate
A Python port of ABRicate, a tool for mass screening of contigs for antibiotic resistance and virulence genes.
pyncbitk
Cython bindings and Python interface to the NCBI C++ Toolkit.
fastobo
Faultless AST for Open Biomedical Ontologies in Python.
gb-io
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
gecco-tool
Gene Cluster prediction with Conditional random fields. (renamed to gecco)
peptides
Physicochemical properties, indices and descriptors for amino-acid sequences.
mininear
A NumPy port of the NEAR code for embedding protein sequences.
pyskani
PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
pyswrd
Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a heuristic method for fast database search.
lightmotif
PyO3 bindings and Python interface to lightmotif, a library for platform-accelerated biological motif scanning using position weight matrices.
pymemesuite
Cython bindings and Python interface to the MEME suite.
igua
Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.
pycomsa
Cython bindings and Python interface to CoMSA, a compressor for multiple-sequence alignments.
orthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement. (renamed to pyorthoani)
pyorthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
nafcodec
PyO3 bindings and Python interface to nafcodec, an encoder/decoder for Nucleotide Archive Format (NAF) files.
pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
sphinxcontrib-svgbob
A Sphinx extension to convert ASCII diagrams to SVGs with Svgbob.
pysylph
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
diced
Rust re-implementation of the MinCED algorithm to Detect Instances of CRISPRs in Environmental Data.
pytantan
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
mini3di
A NumPy port of the foldseek code for encoding structures to 3di.
pyrodigal-gv
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
rlinalg
Linear Algebra routines for Python as implemented in the R language.
torch-treecrf
A PyTorch implementation of Tree-structured Conditional Random Fields.
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
fs.smbfs
Pyfilesystem2 over SMB using pysmb
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.
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.
