103 Open source projects that are alternatives of or similar to ATACseq

HMMRATAC peak caller for ATAC-seq data

Finds SNP sites from a multi-FASTA alignment file

Improve the quality of a denovo assembly by scaffolding and gap filling

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

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

Assembling the cause of phenotypes and genotypes from NGS data

Multilocus sequence typing by blast using the schemes from PubMLST

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Project Manager for NGS data analysis

Audio Fingerprinting and Recognition in Python using NVidia's CUDA

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

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

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Collection of scripts for bacterial genomics

CWL tools and workflows for GGR

All-in-one analysis pipeline

gargammel is an ancient DNA simulator

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

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

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

chromatin Variability Across Regions (of the genome!)

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Minor Variant Calling and Phasing Tools

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

Intuitive local web frontend for the BLAST bioinformatics tool

Sequence lineage information extracted from RKI sequence data repo

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

Analysing Capture Seq Count Data

De novo assembly from Oxford Nanopore reads.

Multi-omics analysis protocols by Lyu.

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

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

The detection of peaks and valleys in a 1d-vector or 2d-array (image)

Command line utility for manipulating Illumina-generated FastQ files.

Rare variant test software for next generation sequencing data

Cloud-based single-cell copy-number variation analysis tool

Rapid large-scale prokaryote pan genome analysis

xHLA: Fast and accurate HLA typing from short read sequence data

Maximum likelihood demultiplexing

A Java API for high-throughput sequencing data (HTS) formats.

Utilities for analyzing next generation sequencing data.

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

FASTQ compression

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Basic workflow for ATAC-seq analysis

Analysis Pipeline for Single Cell ATAC-seq

CUT&RUN and CUT&Tag data processing and analysis

dcHiC: Differential compartment analysis for Hi-C datasets

A repository for setting up a RNAseq workflow

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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

nucleosome calling using ATAC-seq

Tools for analyzing 10X Genomics data