75 Open source projects that are alternatives of or similar to scABC

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Papers with code for single cell related papers

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

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

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Efficient genotyping bi-allelic SNPs on single cells

Convert between AnnData and SingleCellExperiment

Multi-omics analysis protocols by Lyu.

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Single-cell copy number calling and event history reconstruction.

Analysing Capture Seq Count Data

Basic workflow for ATAC-seq analysis

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

ATAC-seq snakemake pipeline

Single cell analysis in the browser

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

A tool that allows to get UMI counts from a single cell protein assay

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

<<------ Use SnapATAC!!

Simulating single-cell data using gene regulatory networks 📠

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

Multiome GRN inference.

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Software for exploration of gene expression data from single-cell RNA sequencing.

Single-Cell Omics Preparation Entity Tools

HMMRATAC peak caller for ATAC-seq data

CUT&RUN and CUT&Tag data processing and analysis

Benchmarking computational single cell ATAC-seq methods

Tools for single-cell data processing

CWL tools and workflows for GGR

A graphical user interface for distributed data processing of high throughput genomics

A toolkit for QC and visualization of ATAC-seq results.

Mouse cell atlas

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

R package to visualize gene expression data based on weighted kernel density estimation

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

Conditional out-of-distribution prediction

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

spatial transcriptome, single cell

All-in-one analysis pipeline

A tool for semi-automatic cell type annotation

Next-Gen Sequencing tools from the Horvath Lab

nucleosome calling using ATAC-seq

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Clone identification from single-cell data

Methods for detecting doublets in single-cell sequencing data

chromatin Variability Across Regions (of the genome!)

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

R package to do the Ligand Receptor Analysis Visualization

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

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

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

mgatk: mitochondrial genome analysis toolkit

R API and htmlwidget for Vitessce