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lucidrains
enformer-pytorch

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

12K 564 101
helicalAI
helical

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

7K 211 37
Edinburgh-Genome-Foundry
sequenticon

:space_invader: Generate identicons for DNA sequences with Python

6K 38 5
UC-Davis-molecular-computing
scadnano

Python scripting library for generating designs readable by scadnano.

2K 16 8
dputhier
pygtftk

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

2K 52 6
dib-lab
kspider

A simple yet powerful sequence clustering tool.

846 8 1
xapple
crest4

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

616 5 1
remytuyeras
haplodynamics

A python library to develop genomic data simulators

526 4 0
graph-part
graph-part

Graph-based partitioning of biological sequence data

511 35 6
jmenglund
predsim

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

410 2 0
tomdstanton
pyeris

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

352 1 1
sgelias
kmergenerator

No description available

352 2 1
kdmurray91
pymer

Fast pythontic k-mer counting routines

319 0 1
Edinburgh-Genome-Foundry
crazydoc

Read DNA sequences from colourful Microsoft Word documents

279 34 4
GeorgakilasLab
cnnamon

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

241 0 0
aszymik
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.

188 3 1
mr-eyes
kspider2

A simple yet powerful sequence clustering tool.

179 8 1
xapple
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.

145 2 0
babinyurii
crispr-cas9

NGS data analysis scripts for HBV elimination research group

129 4 3
UC-Davis-molecular-computing
scadnano-test

Python scripting library for generating designs readable by scadnano.

89 16 8
dabane-ghassan
dnazip-bioinfo

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

66 4 1
NuruddinKhoiry
convertfq

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

49 0 0
MAGICS-LAB
genoarmory

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

34 38 5
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