63 Open Source Gene Expression Software Projects
Free and open source gene expression code projects including engines, APIs, generators, and tools.
Deep Learning Gene Expression23 ⭐
Deep learning methods for feature selection in gene expression autism data.
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
BioBombe: Sequentially compressed gene expression features enhances biological signatures
This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Adversarial Gene Expression10 ⭐
Adversarial generation of gene expression data using Generative Adversarial Networks
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Fishpond: differential transcript and gene expression with inferential replicates. Also, helper functions for working with Salmon/alevin data in Bioconductor, including loadFry() and readEDS()
Awesome Expression Browser77 ⭐
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
Generic Expression Patterns10 ⭐
Distinguishing between generic and experiment-specific gene expression signals.
Combine Lab Salmon518 ⭐
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Catavallejos Basics74 ⭐
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
Breast Cancer Gene Expression32 ⭐
This project aims to predict people who will survive breast cancer using machine learning models with the help of clinical data and gene expression profiles of the patients.
Enformer Pytorch96 ⭐
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Tf Bind Transformer24 ⭐
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
Bohdan Khomtchouk Microscope20 ⭐
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016
Awesome Single Cell1978 ⭐
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Tomkellygenetics Graphsim15 ⭐
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Gfellerlab Epic50 ⭐
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.