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Top 22 gene-expression open source projects

Awesome Single Cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

✭ 1,937

awesome-list data-visualization bioinformatics analysis clustering gene-expression dimensionality-reduction data-integration atac-seq single-cell rna-seq-data scrna-seq-data cell-cycle cell-differentiation gene-expression-profiles analysis-pipeline cell-populations rna-seq-experiments cell-clusters

RNAseq titration results

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

✭ 22

r shell python Dockerfile machine-learning bioinformatics analysis cancer gene-expression rnaseq microarray normalization supplement

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

✭ 19

r genomics gene-expression single-cell

Make rapid visualizations of RNA-seq data in R

✭ 19

r visualization gene-expression rna-seq-analysis differential-expression data-munging

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

✭ 61

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

enformer-pytorch

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

✭ 146

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

Interactive R package to quantify, analyse and visualise alternative splicing

✭ 26

r javascript tcga gene-expression bioconductor alternative-splicing gtex survival splicing-quantification data-analyses differential-splicing-analysis rna-seq-data sra differential-gene-expression vast-tools recount2

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

✭ 33

r C++gene-expression rstats spatial-analysis single-cell spatial-transcriptomics cell-cell-communication

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

✭ 66

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

📊 Gene expression in neuroexpresso database

✭ 15

r javascript CSS visualization bioinformatics shiny neuroscience gene-expression neurobiology neuroinformatics neuron mancarci-2017 neuroexpresso

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

✭ 16

r TeX ruby package benchmarking genomics graph-algorithms genetics gene-expression simulated-data joss simulation-modeling genomic-data-analysis ngs-analysis r-stats gene-regulatory-networks igraph-networks

GREIN : GEO RNA-seq Experiments Interactive Navigator

✭ 40

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

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

✭ 30

python Dockerfile shell systems-biology computational-biology gene-expression metabolism cobra cobrapy metabolic-models

Transcripts annotation and GO enrichment Fisher tests

✭ 24

python shell enrichment genomics gene-expression gene-ontology

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

✭ 31

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Differential Gene Correlation Analysis

✭ 32

r cran rna-seq correlation gene-expression differential-correlation

TCGA data acquisition and processing for Project Cognoma

✭ 17

Jupyter Notebook python shell cancer tcga dataphilly xena xena-browser mutation data-acquisition gene-expression

Spatial alignment of single cell transcriptomic data.

✭ 149

Jupyter Notebook python computational-biology gene-expression scrna-seq spatial-data visium snrna-seq

R package to access DoRothEA's regulons

✭ 98

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

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

✭ 27

python deep-learning gene-expression network-embedding network-representation-learning heterogeneous-data-integration gene-interaction-networks

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

✭ 62

python javascript typescript CSS HTML Dockerfile aws cloud reactjs grpc gene-expression single-cell loom large-scale-data-visualization gene-regulatory-network

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