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gene-expression

Here are 401 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 Oct 1, 2024

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 May 29, 2024
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 cell-cell-communication

Updated Sep 5, 2024
R

lucidrains / enformer-pytorch

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 Oct 9, 2024
Python

broadinstitute / Tangram

Spatial alignment of single cell transcriptomic data.

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

Updated Jun 12, 2024
Jupyter Notebook

junjunlab / ClusterGVis

One-step to Cluster and Visualize Gene Expression Matrix

visualization gene-expression complexheatmap gene-clustering mfuzz

Updated Oct 29, 2024
R

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 Oct 7, 2024
R

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 Oct 27, 2024
C++

saezlab / dorothea

R package to access DoRothEA's regulons

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

Updated Feb 24, 2024
R

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 Oct 25, 2024

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

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 Aug 1, 2023
HTML

Adibvafa / CodonTransformer

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

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

Updated Oct 29, 2024
Python

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 May 28, 2024
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

lucidrains / tf-bind-transformer

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

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 Oct 6, 2024
R

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 Jul 12, 2023
R

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