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

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

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

Deep learning for gene expression inference

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

NicheNet: predict active ligand-target links between interacting cells

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.

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

Building classifiers using cancer transcriptomes across 33 different cancer-types

integrated RNA-seq Analysis Pipeline

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

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

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

BioBombe: Sequentially compressed gene expression features enhances biological signatures

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Gene Expression Omnibus Analysis with Shiny 🔬

Descriptive probabilistic marker gene approach to single-cell pseudotime inference

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

Big data Regression for predicting DNase I hypersensitivity

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

A random-forest-based approach for imputing clustered incomplete data

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

Interactive R package to quantify, analyse and visualise alternative splicing

GEDFN: Graph-Embedded Deep Feedforward Network

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

GREIN : GEO RNA-seq Experiments Interactive Navigator

Transcripts annotation and GO enrichment Fisher tests

Differential Gene Correlation Analysis

ASAP : Automated Single-cell Analysis Pipeline