gene-expression
There are 408 repositories under gene-expression topic.
MixRF
A random-forest-based approach for imputing clustered incomplete data
chromoformer
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
deep-learning-gene-expression
Deep learning methods for feature selection in gene expression autism data.
RNAseq_titration_results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
clonealign
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
RNA-seq-tutorial-for-gene-differential-expression-analysis
This RNAseq data analysis tutorial is created for educational purpose
GNE
This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"
lincs
Library of Integrated Cellular Signatures L1000
BIRD
Big data Regression for predicting DNase I hypersensitivity
fishpond
Differential expression and allelic analysis, nonparametric statistics
ouija
Descriptive probabilistic marker gene approach to single-cell pseudotime inference
RNA-Seq_analysis
scripts for RNA-Seq analysis
adversarial-gene-expression
Adversarial generation of gene expression data using Generative Adversarial Networks
ASAP
ASAP : Automated Single-cell Analysis Pipeline
go_enrichment
Transcripts annotation and GO enrichment Fisher tests
ImmuCC
Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
rna-seq-vae
Variational Auto-Encoder that generates synthetic gene expression data
GEDFN
GEDFN: Graph-Embedded Deep Feedforward Network
Microscope
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
PipeRNAseq
A comprehensive pipeline for RNAseq data analysis
TissUUmapsCore
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.
rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
scINSIGHT
Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
RAPToR
RAPToR (Real Age Prediction from Transcriptome staging on Reference) is a tool to accurately predict individual samples' developmental age from their gene expression profiles.
cancer-data
TCGA data acquisition and processing for Project Cognoma
glmmSeq
Gene-level general linear mixed model
pcaReduce
Code to support: "pcaReduce: hierarchical clustering of single cell transcriptional profiles"
switchde
Inference of switch-like differential expression along single-cell trajectories
vidger
Make rapid visualizations of RNA-seq data in R
neuroexpresso
:bar_chart: Gene expression in neuroexpresso database
GC-SPLeM
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022
tcga-microbiome-prediction
Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.
gEAR
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
DIANE
Dashboard for the Inference and Analysis of Networks from Expression data
BioMM
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data