The Wayback Machine - https://web.archive.org/web/20230313084622/https://github.com/topics/gene-expression

#

gene-expression

Here are 347 public repositories matching this topic...

seandavi / awesome-single-cell

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

Updated Mar 11, 2023

COMBINE-lab / salmon

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

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

Updated Mar 12, 2023
C++

saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

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

Updated Feb 23, 2023
R

lucidrains / enformer-pytorch

Sponsor

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

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

Updated Feb 27, 2023
Python

iSEE / iSEE

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

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

Updated Mar 10, 2023
R

broadinstitute / Tangram

Spatial alignment of single cell transcriptomic data.

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

Updated Feb 9, 2023
Jupyter Notebook

greenelab / tybalt

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

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

Updated Jan 31, 2019
HTML

uci-cbcl / D-GEX

Deep learning for gene expression inference

deep-learning gene-expression

Updated Feb 18, 2019
Python

fbrundu / pymrmr

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

data-science computational-biology gene-expression feature-selection mutual-information

Updated Mar 12, 2023
C++

greenelab / pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

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

Updated Apr 30, 2019
Jupyter Notebook

federicomarini / awesome-expression-browser

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

bioinformatics gene-expression data-visualization awesome-list data-exploration atlas rna-seq-data gene-expression-profiles expression-browser humancellatlas

Updated Nov 16, 2022

saezlab / dorothea

R package to access DoRothEA's regulons

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

Updated Apr 20, 2022
R

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.

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

Updated Jul 15, 2021
R

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

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

Updated Mar 7, 2023
R

nunofonseca / irap

integrated RNA-seq Analysis Pipeline

rna-seq pipeline gene-expression rna-seq-analysis differential-expression transcript-quantification single-cell-rna-seq irap bulk-rna-seq exon-quantification

Updated Feb 6, 2019
R

federicomarini / GeneTonic

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

gui r 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

Updated Mar 10, 2023
R

lucidrains / tf-bind-transformer

Sponsor

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

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

Updated Jun 2, 2022
Python

GfellerLab / EPIC

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

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

Updated Mar 28, 2019
R

greenelab / adage

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

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

Updated May 26, 2016
Python

aertslab / SCope

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

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

Updated Mar 5, 2023
Python

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