Dna Sequences Python Packages

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

scadnano

Python scripting library for generating designs readable by scadnano.

sequenticon

:space_invader: Generate identicons for DNA sequences with Python

pygtftk

The Python GTF toolkit (pygtftk) package: easy handling of GTF files

kspider

A simple yet powerful sequence clustering tool

biocomputing

High-performance DNA sequence generator with Python bindings

codeine

A Python library for constrained reverse translation of protein sequences.

graph-part

Graph-based partitioning of biological sequence data

haplodynamics

A python library to develop genomic data simulators

crest4

The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.

crazydoc

Read genetic sequences from stylized docx files

kmergenerator

No description available

pymer

pymer: Pythonic fast k-mer counting routines

predsim

Command-line tool for simulating predictive datasets from MrBayes' output.

clean-fasta

Clean and filter FASTA sequence files: strip gaps, filter by length and valid-character ratio, and deduplicate ids.

cnnamon

CNNAMON is a modular Python framework for building, training, and interpreting 1D Convolutional Neural Networks (CNNs) for DNA sequence analysis. It integrates data preparation, model construction, and rich explainability tools in a unified and flexible system tailored for genomics research.

jamsfetch

JAMS-Fetch (Joint Automated Multi-source Sequence Fetcher) is a Python package. It automates the retrieval of sequence and structure data from major bioinformatics databases using a unified, user-friendly interface.

crispr-cas9

script for indels counting in sequencing data

kspider2

kSpider Python interface

scadnano-test

Python scripting library for generating designs readable by scadnano.

pacmill

The `pacmill` python package is a bioinformatics pipeline that is developed to process microbial 16S amplicon sequencing data.

filter-classified-reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results

dnazip-bioinfo

A Python implementation of the Burros-Wheeler and Huffman coding algorithms