335 Open source projects that are alternatives of or similar to CUT-RUNTools-2.0

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

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

Bead-based single-cell atac processing

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

mgatk: mitochondrial genome analysis toolkit

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

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

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

High-performance error correction for Illumina resequencing data

Python package and CLI for whole-genome duplication related analyses

GA4GH Variation Representation Python Implementation

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

Genomics Workflows on AWS

Genome Annotation Without Nightmares

DriverPower

Single-cell copy number calling and event history reconstruction.

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Easy genetic ancestry predictions in Python

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Tools for single-cell data processing

A tool for fast and accurate summarizing of variant calling format (VCF) files

Mouse cell atlas

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

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

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

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

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

The GenePattern Server web application

Biopython Jupyter Notebook tutorial to characterize a small genome

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Phage-Host Interaction Search Tool

Convert between AnnData and SingleCellExperiment

simuG: a general-purpose genome simulator

Efficient genotyping bi-allelic SNPs on single cells

Genome-wide imputation pipeline

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

simple viewer for variant call format using htslib

Population assignment analysis using R

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Next-Gen Sequencing tools from the Horvath Lab

Introduction to the Command Line for Genomics

Find target sites for the miRNAs in genomic sequences

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Simulating single-cell data using gene regulatory networks 📠

A secure encryption tool for genomic data

The official code repository for "TensorFlow in Action" by Manning.

Single cell analysis in the browser

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

a pileup library that embraces the huge

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

Seven Bridges Genomics aligner/caller debugging and analysis tools

Large genome reassembly based on Hi-C data, continuation of GRAAL

Finds SNP sites from a multi-FASTA alignment file

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

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