A list of scRNA-seq analysis tools

scRNAseq analysis notes from Ming Tang

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

Variant Library Annotation Tool (VaLiAnT) is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments

ScaleBio Single-cell RNA Nextflow Workflow

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

An R Interface to deck.gl

match command-line arguments to their help text

Graph-linked unified embedding for single-cell multi-omics data integration

Main documentation site for NRNB GSoC project ideas and resources

A project for exploring differentially active signaling paths related to proteomics datasets

R package for detecting doublets in single-cell RNA sequencing data

Unsupervised correction of gene independent cell responses to CRISPR-cas9

Alex Chitsazan's package TITAN for scRNA-seq (Topic Inference of Transcriptionally Associated Networks), an unsupervised Bayesian topic modelling based approach utilizing Latent Dirichlet Allocatio…

R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations

container image to single executable compiler

SLAMSeq processing and analysis pipeline

A comprehensive toolkit for single-cell methylation sequencing data analysis

A package to help convert different single-cell data formats to each other

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…

Context specific and dynamic gene regulatory network reconstruction and analysis

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Streamlining SLAM-seq analysis with ultra-high sensitivity

single cell Flux Estimation Analysis (scFEA) Try the below web server!