Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
-
Updated
Mar 27, 2024
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
Deep learning methods for feature selection in gene expression autism data.
Recurrent Variational Auto gene encoder
Scripts and data from "Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms"
Methods for training and interpreting deep radiogenomic neural networks
A multi-response Gaussian model capable of accurately estimating the composition of blood samples from their gene expression profiles. Fit on Affymetrix Gene ST gene expression profiles using the glmnet R package.
Non-Negative Matrix Factorization for Gene Expression Clustering
SPOT - Swift Profiling Of Transcriptomes - a shiny app for gene ranking according to user-defined expression profiles
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.
NanoString classifier based on NGS training set
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
R package for de novo pathway enrichment using KeyPathwayMiner
Arabidopsis EcoGEx (R-📦 + 🕸️-App)
This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction
SPACEGERM shiny app (archived, see GitLab for active fork)
Shared TREM-1 expression signatures of asthma affection and control
add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects
CMap2 Top Coder Data Science Marathon Match
Add a description, image, and links to the gene-expression-profiles topic page so that developers can more easily learn about it.
To associate your repository with the gene-expression-profiles topic, visit your repo's landing page and select "manage topics."