275 Open source projects that are alternatives of or similar to phylostratr

phenol: Phenotype ontology library

CUT&RUN and CUT&Tag data processing and analysis

Spark VCF data source implementation for Dataframes

A library for manipulating bioinformatics sequencing formats in Apache Spark

simple viewer for variant call format using htslib

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

Ultrafast sequence typing and gene detection from NGS raw reads

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

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

Transcripts annotation and GO enrichment Fisher tests

Big Compute Learning Labs

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

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Forward-time simulation in Python using fwdpp

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Explore gnomAD datasets on the web

Identify phage regions in bacterial genomes for masking purposes

Manhattan plot Generator

Resource of human chromosome schematics & images

Introduction to the Command Line for Genomics

WebAssembly modules for genomics

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

Command line utility for manipulating Illumina-generated FastQ files.

A secure encryption tool for genomic data

Bioconductor package for management of multi-assay data

Python-based UCSC genome browser snapshot-taker and gallery-maker

use the noise

Multilocus sequence typing by blast using the schemes from PubMLST

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

A tool to plot significant regions of GWAS

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

🐳 Bio-dockers: dockerized bioinformatic tools

Explore rearrangements and copy-number amplifications in a cancer genome

Predict AMPs in (meta)genomes and peptides

Bead-based single-cell atac processing

Numerical Encoding for Human Genetic Variants

A fast tool for hybrid genome assembly of long and short reads

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Examples to get started with IBM Functional Genomics Platform

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Analysing Capture Seq Count Data

A package for designing activity-informed nucleic acid diagnostics for viruses.

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

ntHash implementation in Rust

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

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

find large indels (in the blind spot between GATK/freebayes and SV callers)

GA4GH Variation Representation Python Implementation

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

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

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Tools for analyzing 10X Genomics data

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

A fast, scalable, and accurate local ancestry method.

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Nextflow basic tutorial for newbie users