611 Open source projects that are alternatives of or similar to Deeptools

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

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

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

use the noise

DriverPower

WebGL Heatmap Viewer for Big Data and Bioinformatics

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Curated list of bioinformatics formats and publications

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Version 5 of the CAFE phylogenetics software

d3 library to build circular graphs

Feature extraction algorithm for genomic data

GNparser normalises scientific names and extracts their semantic elements.

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Genomics using open source tools, running on GCP or AWS

Genome Annotation Without Nightmares

🎯 Human transcription factor target genes.

Bioinformatics one liners from Ming Tang

This library tackles the construction and efficient execution of computational chemistry workflows

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

simuG: a general-purpose genome simulator

Ploidy agnostic phasing pipeline and algorithm

No description or website provided.

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

A scikit-learn compatible library for graph kernels

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

Read and write FASTQ and FASTA efficiently from Python

Genomics Workflows on AWS

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

Find target sites for the miRNAs in genomic sequences

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

Detection of NCLDV signatures in 'omic data

A library to build and execute typed scientific workflows

Computational Analysis of Novel Drug Opportunities

API for linked biological knowledge

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

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

exploratory and interactive microbiome analyses based on heatmaps

The Ensembl Compara Perl API and SQL schema

Golang for Bioinformatics

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Fast motif matching in R

My collection of light bioinformatics analysis pipelines for specific tasks

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Find causal cell-types underlying complex trait genetics

A modular annotation tool for genomic variants

Environmental DNA metabarcoding taxonomic identification

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

pythonic wrapper for htslib

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Home of the Genomic Feature and Variation Ontology (GFVO)

A simple tool to calculate reads number and total base count in FASTQ file

Bioinformatics containers

Reference-based transcript discovery from long RNA read