Projects in Awesome Lists tagged with gene-expression

https://github.com/COMBINE-lab/salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

10x bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq sailfish salmon scrna-seq selective-alignment single-cell single-cell-rna-seq transcriptome

Last synced: 11 May 2025

https://github.com/saeyslab/nichenetr

NicheNet: predict active ligand-target links between interacting cells

cell-cell-communication data-integration gene-expression intercellular-communication ligand-receptor ligand-target network-inference rna-seq single-cell-omics single-cell-rna-seq

Last synced: 13 Mar 2026

https://github.com/lucidrains/enformer-pytorch

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

artificial-intelligence attention-mechanism deep-learning dna-sequences gene-expression genomics transformer

Last synced: 15 May 2025

https://github.com/broadinstitute/Tangram

Spatial alignment of single cell transcriptomic data.

computational-biology gene-expression scrna-seq snrna-seq spatial-data visium

Last synced: 20 Apr 2025

https://github.com/broadinstitute/tangram

Spatial alignment of single cell transcriptomic data.

computational-biology gene-expression scrna-seq snrna-seq spatial-data visium

Last synced: 12 Apr 2025

https://github.com/isee/isee

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 20 Oct 2025

https://github.com/iSEE/iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 30 Jul 2025

https://github.com/helicalAI/helical

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

artificial-intelligence bioinformatics biology deep-learning dna-sequences evo2 foundation-models gene-expression geneformer helixmrna pre-trained-model pre-training rna rna-seq rnaseq scgpt transcriptformer transformer uce vcf

Last synced: 27 May 2026

https://github.com/greenelab/tybalt

Training and evaluating a variational autoencoder for pan-cancer gene expression data

analysis autoencoder cancer cancer-genomics deep-learning gene-expression script tool unsupervised-learning variational-autoencoder variational-autoencoders

Last synced: 06 Mar 2026

https://github.com/saezlab/dorothea

R package to access DoRothEA's regulons

bioconductor-package functional-analysis gene-expression regulons tf-activities transcription-factor

Last synced: 02 Mar 2025

https://github.com/adibvafa/codontransformer

CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.

bioinformatics biotechnology codon codon-optimization codon-optimizer computational-biology deep-learning gene-expression machine-learning synthetic-biology

Last synced: 12 Apr 2025

https://github.com/greenelab/pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

analysis cancer classifier gene-expression machine-learning methodology pancancer tcga tool transcriptome

Last synced: 05 May 2025

https://github.com/bvieth/powsimR

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.

experimental-design gene-expression power power-analysis r rna-seq simulation simulation-framework single-cell

Last synced: 11 May 2025

https://bvieth.github.io/powsimR/

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.

experimental-design gene-expression power power-analysis r rna-seq simulation simulation-framework single-cell

Last synced: 08 Apr 2025

https://github.com/lucidrains/tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

artificial-intelligence attention-mechanism deep-learning gene-expression transcription-factor-binding transcription-factors transformers

Last synced: 04 Oct 2025

https://github.com/catavallejos/basics

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

bayesian bioconductor-package gene-expression r rcpp rcpparmadillo scrna-seq single-cell

Last synced: 06 Apr 2025

https://github.com/catavallejos/BASiCS

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

bayesian bioconductor-package gene-expression r rcpp rcpparmadillo scrna-seq single-cell

Last synced: 08 Apr 2025

https://github.com/federicomarini/genetonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly

Last synced: 13 Apr 2025

https://github.com/GfellerLab/EPIC

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

bulk-data cancer-cells cell-type gene-expression rna-seq

Last synced: 11 May 2025

https://github.com/aertslab/SCope

Fast visualization tool for large-scale and high dimensional single-cell data

aws cloud gene-expression gene-regulatory-network grpc large-scale-data-visualization loom reactjs single-cell

Last synced: 09 Apr 2025

https://github.com/greenelab/biobombe

BioBombe: Sequentially compressed gene expression features enhances biological signatures

autoencoder biobombe compression gene-expression gene-sets hetnet msigdb network tcga

Last synced: 13 Oct 2025

https://github.com/greenelab/adage

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

autoencoders data dataset denoising-autoencoders gene-expression machine-learning manuscript methodology neural-networks paper pseudomonas-aeruginosa research supplement

Last synced: 07 Mar 2026

https://github.com/uc-bd2k/GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

bioinformatics-analysis bioinformatics-pipeline gene-expression gene-expression-omnibus geo geo-data-processing graphical-interface grein interactive-analysis interactive-visualizations processing r rna-seq rna-seq-analysis rna-seq-data rna-seq-pipeline shiny-apps

Last synced: 06 May 2025

https://github.com/pinellolab/haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

cell chip-seq encode epigenetics epigenomics fimo gene gene-expression haystack-bio haystack-pipeline hotspot motif motifs plasticity regulation rna-seq roadmap specific-regions tfs transcription-factor-binding

Last synced: 06 Feb 2026

https://github.com/SUwonglab/PECA

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

atac-seq chromatin-accessibiity dnase-seq gene-expression gene-regulatory-network rna-seq

Last synced: 20 Nov 2025

https://github.com/drostlab/mytai

Evolutionary Transcriptomics with R

biological-processes conservation evo-devo evolution evolutionary-transcriptomics expression-profiles gene-expression gene-sets mytai r studies-transcriptomes transcriptome

Last synced: 05 Apr 2025

https://github.com/jasdumas/shinygeo

Gene Expression Omnibus Analysis with Shiny :microscope:

bioinformatics data-visualization gene-expression r shiny

Last synced: 05 Mar 2025

https://github.com/jasdumas/shinyGEO

Gene Expression Omnibus Analysis with Shiny :microscope:

bioinformatics data-visualization gene-expression r shiny

Last synced: 05 May 2025

https://github.com/tlatkowski/deep-learning-gene-expression

Deep learning methods for feature selection in gene expression autism data.

annotated-genes autism autism-data data-mining deep-learning feature-detection feature-extraction feature-selection features-extraction fisher-score gene-annotation gene-expression gene-expression-profiles google-colab microarray-data ncbi-database neural-network numpy python3 ttest

Last synced: 30 Apr 2025

https://github.com/greenelab/rnaseq_titration_results

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

analysis bioinformatics cancer gene-expression machine-learning microarray normalization rnaseq supplement

Last synced: 07 Mar 2026

https://github.com/kieranrcampbell/clonealign

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

cancer-genomics gene-expression single-cell

Last synced: 25 Dec 2025

https://github.com/randel/MixRF

A random-forest-based approach for imputing clustered incomplete data

gene-expression imputation mixed-models random-forest

Last synced: 26 Apr 2025

https://github.com/dohlee/chromoformer

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

artificial-intelligence bioinformatics deep-learning epigenomics gene-expression genomics histone-modifications transcriptomics transformer

Last synced: 29 Apr 2025

https://github.com/dhimmel/lincs

Library of Integrated Cellular Signatures L1000

gene-expression l1000 lincs rephetio

Last synced: 11 Sep 2025

https://github.com/kieranrcampbell/ouija

Descriptive probabilistic marker gene approach to single-cell pseudotime inference

bayesian-methods factor-analysis gene-expression single-cell

Last synced: 25 Dec 2025

https://github.com/rvinas/adversarial-gene-expression

Adversarial generation of gene expression data using Generative Adversarial Networks

adversarial-machine-learning adversarial-networks bioinformatics e-coli gan gene-expression gene-regulatory-network generative-adversarial-network keras machine-learning tensorflow

Last synced: 18 Mar 2025

https://github.com/myles-lewis/glmmseq

Gene-level general linear mixed model

bioinformatics cran differential-gene-expression gene-expression glmm mixed-models transcriptomics

Last synced: 22 Oct 2025

https://github.com/kieranrcampbell/switchde

Inference of switch-like differential expression along single-cell trajectories

gene-expression genomics single-cell

Last synced: 20 Oct 2025

https://github.com/transbiozi/biomm

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

biomm dna-methylation elasticnetregression epigenomics gene-expression genomics go-pathway gwas high-dimensional kegg-pathway machine-learning omics phenotype-prediction random-forest svm transcriptomics

Last synced: 24 Feb 2026

https://github.com/greenelab/gbm_immune_validation

Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors

analysis cancer data-science gene-expression glioblastoma machine-learning survival-analysis tool

Last synced: 07 Jul 2025

https://github.com/almeidasilvaf/hybridexpress

An R package for comparative transcriptomic analyses of hybrids and their progenitors

gene-expression hybrid polyploidy rna-seq transcriptomics

Last synced: 18 Feb 2026

https://github.com/OceaneCsn/DIANE

Dashboard for the Inference and Analysis of Networks from Expression data

analysis-workflows gene-expression network-inference r

Last synced: 30 Jul 2025

https://github.com/greenelab/generic-expression-patterns

Distinguishing between generic and experiment-specific gene expression signals.

analysis autoencoder gene-expression machine-learning neural-network pseudomonas-aeruginosa software variational-autoencoder

Last synced: 05 May 2025

https://github.com/bgeedb/bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database

affymetrix biology est expression gene gene-expression in-situ-hybridization java makefile perl pipeline python rna-seq transcriptomics

Last synced: 20 Feb 2026

https://github.com/clauswilke/pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates

codons gene-expression gillespie-algorithm stochastic-simulation transcription translation

Last synced: 22 Mar 2025

https://github.com/soedinglab/tejaas

Tejaas - a tool for discovering trans-eQTLs

eqtl eqtl-mapping gene-expression gtex reverse-regression trans-eqtl

Last synced: 27 Apr 2025

https://github.com/maayanlab/playbook-workflow-builder

A repository for the Playbook Workflow Builder project.

bioinformatics biology cwl data-science gene-expression gene-ontology gene-sets proteomics rna-seq-analysis systems-biology workflow

Last synced: 11 Jul 2025

https://github.com/greenelab/hgsc_subtypes

Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four

cancer gene-expression machine-learning methodology ovarian-cancer subtype

Last synced: 05 May 2025

https://github.com/greenelab/nf1_inactivation

Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation

analysis cancer gene-expression machine-learning methodology

Last synced: 04 Jul 2025

https://github.com/chen0040/java-genetic-programming

Genetic-programming framework for various genetic programming paradigms such as linear genetic programming, tree genetic programming, gene expression programming, etc

classification-algorithm evolutionary-algorithms evolutionary-computation gene-expression genetic-programming java linear-genetic-programming machine-learning optimization optimization-algorithms symbolic-regression tree-gp

Last synced: 10 Sep 2025

https://github.com/nalomran/pyreqtl

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.

bioinformatics bioinformatics-analysis bioinformatics-tool data-science gene-expression matrixeqtl numpy pandas python python3 r rna-seq rna-seq-analysis rpy2 scipy snvs

Last synced: 27 Oct 2025

https://github.com/saeyslab/nichenetpy

cell-cell-communication data-integration gene-expression intercellular-communication ligand-receptor ligand-target network-inference rna-seq single-cell-omics single-cell-rna-seq

Last synced: 12 Jul 2026

https://github.com/greenelab/pancancer-evaluation

Evaluating genome-wide prediction of driver mutations using pan-cancer data

analysis cancer classifier gene-expression genome machine-learning pancancer

Last synced: 05 May 2025

https://github.com/bhklab/survcomp

R package for performance assessment and comparison for survival analysis

differential-expression gene-expression regression survival visualization

Last synced: 13 Apr 2025

https://github.com/reese3928/rnaagecalc

A multi-tissue transcriptional age calculator

biological-age elastic-net gene-expression genotype-tissue-expression prediction regularized-regression rna-seq

Last synced: 20 Feb 2026

https://github.com/drisso/archive-ruvseq

Archived version of RUVSeq

gene-expression normalization r rna-seq statistical-models

Last synced: 07 Sep 2025

https://github.com/jware-solutions/ggca

Blazing fast Gene/GEM Correlation Analysis for Rust and Python

bioinformatic correlation correlation-analysis gene-expression gene-expression-modulation python rust

Last synced: 31 Mar 2025

https://github.com/nanxstats/grex

Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data

bioinformatics gene-expression genotype-tissue-expression gtex

Last synced: 22 Apr 2025

https://github.com/greenelab/tdmresults

Scripts and data for re-creating TDM results.

dataset gene-expression results supplement

Last synced: 05 May 2025

https://github.com/greenelab/pathcore-t-analysis

This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.

feature-extraction gene-expression pathway-analysis supplement

Last synced: 05 May 2025

https://github.com/greenelab/gea_community_detection

Overrepresentation analysis for KEGG and PID pathways using community detection

analysis detection-network enrichment-analysis gene-expression kegg-pathway networks pathway pathway-analysis pid

Last synced: 05 May 2025

https://github.com/bhklab/metagx

Scripts to perform meta-analysis of cancer gene expression datasets

gene-expression meta-analysis

Last synced: 13 Apr 2025

https://github.com/htpusa/moomin

MOOMIN is a tool for analysing differential expression data

constraint-based-modeling differential-expression gene-expression matlab metabolic-network moomin

Last synced: 13 Oct 2025

https://github.com/dmmiller612/correlation-gcn

Correlation Graph Convolutional Networks on Gene Expression and other Biology data

deep-learning gcn gene gene-expression graph graph-convolutional-network proteomics tensorflow

Last synced: 29 Oct 2025

https://github.com/nuno-agostinho/ctrap

Identification of candidate causal perturbations from differential gene expression data

bioconductor bioinformatics cmap gene-expression l1000 r r-package

Last synced: 18 Aug 2025

https://github.com/cai-lab-at-university-of-michigan/micv

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

anndata clustering gene-expression leiden marker-genes pseudotime pseudotime-trajectory scanpy umap-projection

Last synced: 05 May 2026

https://github.com/drisso/archive-zinbwave

Archived version of the zinbwave package. All future development will be done on https://github.com/drisso/zinbwave

gene-expression r rna-seq single-cell single-cell-genomics statistical-models

Last synced: 07 Sep 2025

https://github.com/greenelab/stanmf

A python implementation of Stability NMF

analysis gene-expression machine-learning tool

Last synced: 05 May 2025

https://github.com/greenelab/rheum-plier-data

Data repository for the MultiPLIER project

dataset gene-expression tool

Last synced: 06 Aug 2025

https://github.com/slowkow/saturation

:sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

10xgenomics bioinformatics gene-expression ngs-analysis vdj

Last synced: 28 Jul 2025

https://github.com/greenelab/linear_signal

Comparing the performance of linear and nonlinear models in transcriptomic prediction

analysis deep-learning gene-expression machine-learning tool

Last synced: 04 Jul 2025

https://github.com/greenelab/pathcore-t

Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.

analysis gene-expression methodology supplement

Last synced: 05 May 2025

https://github.com/pentalpha/r-peridot

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

bioconductor bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-tool differential-expression differential-expression-analysis gene-expression rna-seq-analysis rna-seq-pipeline

Last synced: 15 May 2026

https://github.com/greenelab/greedy-geneset-selection

Source code associated with "Leveraging global gene expression patterns to predict expression of unmeasured genes"

cancer gene-expression methodology

Last synced: 17 Jun 2025

https://github.com/htpusa/moomin.jl

From differential gene expression to metabolic changes

constraint-based-modeling differential-expression gene-expression metabolic-models transcriptomics

Last synced: 11 Apr 2025

https://github.com/greenelab/adage-frontend

The Adage web app, a tool to explore gene expression data and discover new insights from machine learning models

bioinformatics gene-expression genomics machine-learning research science web-app

Last synced: 05 May 2025

https://github.com/tripal/tripal_analysis_expression

Extension module for the Tripal toolset to show differential expression data. This module was made for Drupal 7, Tripal 3, and Chado 1.3.

analysis chado gene-expression loader tripal

Last synced: 05 Apr 2025

https://github.com/le-ander/msc_bioinfo-network_inference

Network inference for gene expression using gradient matching. Final research project as part of the MSc in Bioinformatics and Theorectical Systems Biology at Imperial College London 2016/2017.

bioinformatics gaussian-processes gene-expression gradient-matching julia network-inference systems-biology