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The Top 22 Python Gene Expression Open Source Projects

Open source projects categorized as Python Gene Expression
Categories > Gene Expression
Awesome Single Cell ⭐ 2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
most recent commit 3 months ago
Enformer Pytorch ⭐ 359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 98most recent commit 4 months agopypi enformer-pytorch} Downloads
D Gex ⭐ 117
Deep learning for gene expression inference
most recent commit 5 years ago
Scope ⭐ 56
Fast visualization tool for large-scale and high dimensional single-cell data
most recent commit 2 years ago
Tf Bind Transformer ⭐ 45
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
total releases 94most recent commit 2 years ago
Scnanogps ⭐ 29
Single cell Nanopore sequencing data for Genotype and Phenotype
most recent commit 3 months ago
Cobrame ⭐ 29
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
most recent commit 5 years ago
Chromoformer ⭐ 24
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
total releases 4most recent commit 8 months ago
Go_enrichment ⭐ 23
Transcripts annotation and GO enrichment Fisher tests
most recent commit a year ago
Gedfn ⭐ 19
GEDFN: Graph-Embedded Deep Feedforward Network
most recent commit 5 years ago
Rnaseq Pipeline ⭐ 18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
most recent commit 3 months ago
Gne ⭐ 13
This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"
most recent commit 3 years ago
Mybmonday ⭐ 10
MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets
most recent commit 9 months ago
Deep Learning Gene Expression ⭐ 10
Deep learning methods for feature selection in gene expression autism data.
most recent commit 5 years ago
Pyreqtl ⭐ 9
A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.
total releases 2most recent commit 4 years ago
Rna Seq Vae ⭐ 9
Synthetic gene expression data generation using Variational Auto-Encoder
most recent commit a year ago
Bgee_pipeline ⭐ 8
Source code of the Bgee pipeline used to build the Bgee database
most recent commit a year ago
Genome_integration ⭐ 8
MR-link and genome integration. genome_integration is a repository for the analysis of genomic data. Specifically, the repository implements the causal inference method MR-link, as well as other Mendelian randomization methods.
most recent commit 2 years ago
Gc Splem ⭐ 8
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022
most recent commit a year ago
Rna Seek ⭐ 8
A comprehensive quality-control and quantification RNA-seq pipeline
most recent commit 3 months ago
Orthomap ⭐ 6
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
total releases 1most recent commit 5 months ago
Modulector ⭐ 5
An open platform which provides information about miRNAs and genes from different popular databases
most recent commit 3 months ago
The 5 Latest Releases In Python Gene Expression Open Source Projects
Enformer Pytorch ⭐ 359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 98latest release November 03, 2023most recent commit 4 months agopypi enformer-pytorch} Downloads
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