1083 Open source projects that are alternatives of or similar to wdlRunR

Proof-of-concept seq-to-graph mapper and graph generator

🎯 Human transcription factor target genes.

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

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

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Bystro genetic analysis (annotation, filtering, statistics)

JavaScript VisualizationTools

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A curated list of awesome bioinformatics software.

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

A fast 23andMe genome text file parser, now superseded by arv

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

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

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

annotate a VCF with other VCFs/BEDs/tabixed files

De novo assembly based variant calling pipeline for Illumina short reads

A high-performance, Pythonic language for bioinformatics

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Efficient pythonic random access to fasta subsequences

BACNET is a Java based platform to develop website for multi-omics analysis

Python library to facilitate genome assembly, annotation, and comparative genomics

A modern genome browser built with JavaScript and HTML5.

Tools to process and analyze deep sequencing data.

A fast and sensitive gapped read aligner

Data intensive science for everyone.

Scalable genomic data analysis.

A collection of publications on comparison of high-throughput sequencing technologies.

A curated list of bioinformatics bench-marking papers and resources.

Model and predict short DNA sequence features with neural networks

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

An interactive web tool for quality control of DNA sequencing data

Analysis pipelines for sequencing data

Genomics Extension for SQLite

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Antimicrobial Resistance Identification By Assembly

Lightweight Iterative Gene set Enrichment in R

NGLess: NGS with less work

A cool place to store your Hi-C

A tool to circularize genome assemblies

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Bioconductor package for management of multi-assay data

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Bayesian haplotype-based mutation calling

Official code repository for GATK versions 4 and up

Rapid large-scale prokaryote pan genome analysis

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Deep learning infrastructure for bioinformatics

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools

Interactive assembly and analysis of RAD-seq data sets

Grammar of Scalable Linked Interactive Nucleotide Graphics

An R framework for phylostratigraphy

PERF is an Exhaustive Repeat Finder

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

Tools for analyzing 10X Genomics data

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