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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
jware-solutions
ggca

Blazing fast Gene/GEM Correlation Analysis for Rust and Python

6K 10 3
adibvafa
codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

4K 206 31
lucidrains
tf-bind-transformer

Transformer for Transcription Factor Binding

3K 88 9
broadinstitute
tangram-sc

Spatial alignment of single cell transcriptomic data.

3K 362 64
mzguntalan
z-zytome

Zytome is declarative library for handling gene expression data for various data portals or datasets.

1K 3 1
fbrundu
pymrmr

Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

1K 141 37
sanjaynagi
anoexpress

A package to access insecticide resistance gene expression meta analyse in Anopheles mosquitoes

1K 5 0
mvinyard
vintools

Michael Vinyard's utilities

772 2 2
YifeiSheng
cytocraft

The Cytocraft package provides prediction of chromosome configuration based on subcellular resolution spatial transcriptomics.

599 0 0
greenelab
ponyo

Software to simulate compendium-wide gene expression data using a VAE.

396 3 3
srp33
shapeshifter

A tool for managing large datasets

237 2 5
greenelab
stanmf

A python implementation of Stability NMF

224 6 3
cafferychen777
flashs

Flash-S: Frequency-domain Linearized Adaptive Spatial Hypothesis testing via Sketching

202 0 0
clauswilke
pinetree

stochastic simulation of gene expression with site-specific translation rates

190 12 5
srp33
shapeshifter-cli

A command-line tool for transforming large data sets

187 2 0
dohlee
chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

186 38 2
brycetolman54
ccbcge

Python package to access Breast Cancer Gene Expression data

173 1 0
srp33
expressionable

A tool for managing large datasets

166 2 5
srp33
expressionable-cli

A command-line tool for transforming large data sets

157 2 0
saroudant
sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

155 6 2
bio2bel
bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

102 1 0
princello
ncountr

Python pipeline for Nanostring nCounter data analysis

92 2 0
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