90 Open source projects that are alternatives of or similar to gchromVAR

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

No description or website provided.

mgatk: mitochondrial genome analysis toolkit

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

Bead-based single-cell atac processing

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

CUT&RUN and CUT&Tag data processing and analysis

Rare variant test software for next generation sequencing data

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Visual Machine Learning of Genome-Phenome Associations

Clone identification from single-cell data

Conditional out-of-distribution prediction

Mixed models @lme4 + custom covariances + parameter constraints

Next-Gen Sequencing tools from the Horvath Lab

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

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

Tools for single-cell data processing

HMMRATAC peak caller for ATAC-seq data

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

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

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

GWAS summary statistics files QC tool

Python API for comprehensive GWAS analysis using GEMMA

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

Convert between AnnData and SingleCellExperiment

Adjacency-constrained hierarchical clustering of a similarity matrix

Detecting methylation using signal-level features from Nanopore sequencing reads

Single-Cell Omics Preparation Entity Tools

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

A tool for semi-automatic cell type annotation

Single-cell copy number calling and event history reconstruction.

Analysing Capture Seq Count Data

Simulating single-cell data using gene regulatory networks 📠

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

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

Efficient genotyping bi-allelic SNPs on single cells

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

chromatin Variability Across Regions (of the genome!)

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

R package to do the Ligand Receptor Analysis Visualization

CWL tools and workflows for GGR

📊 Identify cell types and pathways affected by genetic risk loci.

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

Find causal cell-types underlying complex trait genetics

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

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

Quantitative Trait Cluster Association Test in R

Heritability, genetic correlation and functional enrichment estimation for case-control studies

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

Mouse cell atlas

A faster lmm for GWAS. Supports GPU backend.

Perform GWAS using the FarmCPU model.

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

Single cell analysis in the browser

Modelling DNA methylation profiles

Basic workflow for ATAC-seq analysis

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

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

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