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

Modelling DNA methylation profiles

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

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

Benchmarking computational single cell ATAC-seq methods

ATAC-seq snakemake pipeline

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

nucleosome calling using ATAC-seq

Experimental design framework for scRNAseq population studies (eQTL and DE)

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Dynamical systems methods for RNA velocity analysis

Inference of switch-like differential expression along single-cell trajectories

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Reference mapping for single-cell genomics

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Manuscript for functional prediction of transcriptomic “dark matter” across species

Papers with code for single cell related papers

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

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

spatial transcriptome, single cell

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

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

Methods for detecting doublets in single-cell sequencing data

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

Multiome GRN inference.

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

R API and htmlwidget for Vitessce