Dna Sequences Python Packages

enformer-pytorch

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

12K 564 101

helical

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

7K 211 37

sequenticon

:space_invader: Generate identicons for DNA sequences with Python

7K 38 5

scadnano

Python scripting library for generating designs readable by scadnano.

2K 16 8

pygtftk

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

2K 52 6

kspider

A simple yet powerful sequence clustering tool.

770 8 1

crest4

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

554 5 1

haplodynamics

A python library to develop genomic data simulators

528 4 0

graph-part

Graph-based partitioning of biological sequence data

507 35 6

predsim

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

402 2 0

pyeris

🧬🍏✨ Graph-aware contextual annotation of targeted genomic features.

378 1 1

kmergenerator

No description available

365 2 1

pymer

Fast pythontic k-mer counting routines

338 0 1

crazydoc

Read DNA sequences from colourful Microsoft Word documents

258 34 4

cnnamon

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

242 0 0

jamsfetch

Package for automatic data download from major bioinformatics databases

203 3 1

kspider2

A simple yet powerful sequence clustering tool.

174 8 1

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.

150 2 0

crispr-cas9

NGS data analysis scripts for HBV elimination research group

124 4 3

scadnano-test

Python scripting library for generating designs readable by scadnano.

99 16 8

dnazip-bioinfo

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

80 4 1

convertfq

Converting DNA to RNA or RNA to DNA in a fastq file

47 0 0

genoarmory

GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models

37 38 5