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Dna Sequences Python Packages

Python packages with the GitHub topic dna-sequences. Sorted by relevance, with stars and monthly downloads.
lucidrains
enformer-pytorch

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

11K 564 101
Edinburgh-Genome-Foundry
sequenticon

:space_invader: Generate identicons for DNA sequences with Python

6K 38 5
helicalAI
helical

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

6K 214 37
sigdelsanjog
biocomputing

pip install biocomputing

3K 0 0
UC-Davis-molecular-computing
scadnano

Python scripting library for generating designs readable by scadnano.

2K 16 8
dputhier
pygtftk

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

1K 52 6
remytuyeras
haplodynamics

A python library to develop genomic data simulators

618 4 0
xapple
crest4

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

617 5 1
dib-lab
kspider

A simple yet powerful sequence clustering tool.

465 8 1
sgelias
kmergenerator

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

447 2 1
graph-part
graph-part

GraphPart, a data partitioning method for ML on biological sequences

442 35 6
tomdstanton
pyeris

Graph-aware contextual annotation of targeted genomic features

429 1 1
Edinburgh-Genome-Foundry
crazydoc

Read DNA sequences from colourful Microsoft Word documents

368 34 4
GeorgakilasLab
cnnamon

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

339 0 0
jmenglund
predsim

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

286 2 0
peterk87
filter-classified-reads

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

286 7 1
kdmurray91
pymer

pymer: Pythonic fast k-mer counting routines

255 0 1
aszymik
jamsfetch

Package for automatic data download from major bioinformatics databases

187 3 1
babinyurii
crispr-cas9

NGS data analysis scripts for HBV elimination research group

175 4 3
mr-eyes
kspider2

A simple yet powerful sequence clustering tool.

135 8 1
xapple
pacmill

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

109 2 0
UC-Davis-molecular-computing
scadnano-test

Python scripting library for generating designs readable by scadnano.

101 16 8
dabane-ghassan
dnazip-bioinfo

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

80 4 1
NuruddinKhoiry
convertfq

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

54 0 0
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