404 Open source projects that are alternatives of or similar to polyRAD

Genotyping of segregating mobile elements insertions

Stacked Denoising AutoEncoder based on TensorFlow

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Feature extraction algorithm for genomic data

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Highly customizable, ambiguity-aware dotplots for visual sequence analyses

A curated list of resources for machine learning for small-molecule drug discovery

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

Rapid determination of appropriate reference genomes.

Ploidy agnostic phasing pipeline and algorithm

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

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Genomics data visualization in Python by using matplotlib.

Mulled - Automatized Containerized Software Repository

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

MView extracts and reformats the results of a sequence database search or multiple alignment.

Assembling the cause of phenotypes and genotypes from NGS data

Version 5 of the CAFE phylogenetics software

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

🎯 Human transcription factor target genes.

GWAS summary statistics files QC tool

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

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

API for linked biological knowledge

Golang for Bioinformatics

Fast and flexible ORF finder

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An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

Sentieon DNAseq

Method to optimally select samples for validation and resequencing

A computational library for learning and evaluating biological knowledge graph embeddings

Fast motif matching in R

Simple pure Python SAM parser and objects for working with SAM records

Compute N50/NG50 and auN/auNG

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

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

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

WebGL Heatmap Viewer for Big Data and Bioinformatics

Provide R access to the NCI Genomic Data Commons portal.

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

A library to build and execute typed scientific workflows

A package for designing compact and comprehensive capture probe sets.

Useful bioinformatic scripts

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Read DNA sequences from colourful Microsoft Word documents

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

My own tools code for NGS data analysis (Next Generation Sequencing)

Read and write FASTQ and FASTA efficiently from Python

React rerelease of MSAViewer

Fast hash function for DNA sequences

An open-access bioinformatics text

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

Fast alignment and preprocessing of chromatin profiles

Unsupervised domain adaptation method for relation extraction

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

exploratory and interactive microbiome analyses based on heatmaps

A curated list of awesome bioinformatics software.

Per-base per-nucleotide depth analysis

3D printed sculpture of a DNA molecule, showing my own genome