Dna Sequences Python Packages

enformer-pytorch

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

sequenticon

:space_invader: Generate identicons for DNA sequences with Python

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.

biocomputing

pip install biocomputing

pygtftk

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

kspider

A simple yet powerful sequence clustering tool.

crest4

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

haplodynamics

A python library to develop genomic data simulators

cnnamon

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

graph-part

GraphPart, a data partitioning method for ML on biological sequences

kmergenerator

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

filter-classified-reads

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

crazydoc

Read genetic sequences from stylized docx files

pymer

pymer: Pythonic fast k-mer counting routines

predsim

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

jamsfetch

Package for automatic data download from major bioinformatics databases

crispr-cas9

script for indels counting in sequencing data

kspider2

A simple yet powerful sequence clustering tool.

pacmill

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

dnazip-bioinfo

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

scadnano-test

Python scripting library for generating designs readable by scadnano.

pyeris

Graph-aware contextual annotation of targeted genomic features

convertfq

convertFQ is used to convert either DNA2RNA or RNA2DNA in a fastq file