165 Open source projects that are alternatives of or similar to rvtests

Spark VCF data source implementation for Dataframes

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Multi-sample somatic variant caller

A phenotype-based tool for variant prioritization in WES and WGS data

Utilities for analyzing next generation sequencing data.

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

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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.

Genetics (Initialization, Selection, Crossover, Mutation)

Visual Machine Learning of Genome-Phenome Associations

CellRank for directed single-cell fate mapping

No description or website provided.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Fast API server for calculating linkage disequilibrium

Find causal cell-types underlying complex trait genetics

Quantitative Trait Cluster Association Test in R

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

A collection of Galaxy-related training material

Tools for working with genomic and high throughput sequencing data.

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

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

This is the code behind the www.impute.me site. It contains algorithms for personal genome analysis, including imputation and polygenic risk score calculation

R package for analyzing single-cell RNA-seq data

UGENE is free open-source cross-platform bioinformatics software

A standalone and free application to explore genetics variations from VCF file

Sequana: a set of Snakemake NGS pipelines

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

Perform GWAS using the FarmCPU model.

Forward-time simulation in Python using fwdpp

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Manhattan plot Generator

Mixed models @lme4 + custom covariances + parameter constraints

Genome-wide imputation pipeline

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Customizable workflows based on snakemake and python for the analysis of NGS data

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

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

GWAS summary statistics files QC tool

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

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

RNA-seq workflow using STAR and DESeq2

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

NGLess: NGS with less work

A curated list of awesome bioinformatics software.

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Python API for comprehensive GWAS analysis using GEMMA

Code to compute the XP-CLR statistic to infer natural selection

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

A method for variant graph genotyping based on exact alignment of k-mers

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

Heritability, genetic correlation and functional enrichment estimation for case-control studies

Binomica Public Repository for Biological Parts

ABRA2

Official code repository for GATK versions 4 and up

Pyro models of SARS-CoV-2 variants

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Adjacency-constrained hierarchical clustering of a similarity matrix

Resource of human chromosome schematics & images