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

A python package and a set of shell commands to handle GTF files

kspider

A simple yet powerful sequence clustering tool.

biocomputing

pip install biocomputing

codeine

Codeine is a Python library for constrained reverse translation of protein sequences.

graph-part

GraphPart, a data partitioning method for ML on biological sequences

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 DNA sequences from colourful Microsoft Word documents

kmergenerator

Get a kmer list given a single DNA or RNA sequence.

pymer

Fast pythontic k-mer counting routines

predsim

Simulate predictive datasets from MrBayes' output

clean-fasta

A small, dependency-free command-line tool (and Python library) for cleaning and filtering FASTA sequence files. It strips gaps and whitespace, drops sequences that are too short, too long, malformed, or below a valid-character threshold, optionally removes duplicate identifiers, and writes tidy, line-wrapped FASTA output, along with a report.

cnnamon

CNNAMON: a convolutiIonal neural network interpretability framework for deciphering regulatory motif insights

jamsfetch

Package for automatic data download from major bioinformatics databases

crispr-cas9

NGS data analysis scripts for HBV elimination research group

kspider2

A simple yet powerful sequence clustering tool.

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 and produce PDF reports detailing taxonomical assignments along with other statistics.

filter-classified-reads

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

dnazip-bioinfo

A Python implementation of The Burrows-Wheeler Transform alongside Huffman coding on DNA sequences.