612 Open source projects that are alternatives of or similar to streamformatics

A simplified pipeline for ctDNA sequencing data analysis

Sentieon DNAseq

A fast 23andMe genome text file parser, now superseded by arv

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.

Sample search by metadata and features

Read DNA sequences from colourful Microsoft Word documents

SVG based pedigree chart module for webtrees genealogy application.

Fast alignment and preprocessing of chromatin profiles

Phylogenetic trees in Julia

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

Graph Explorer

A computational library for learning and evaluating biological knowledge graph embeddings

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

A treemap interactive chart web component for visualizing hierarchical data

A package for designing compact and comprehensive capture probe sets.

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.

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Provide R access to the NCI Genomic Data Commons portal.

Examples using Clustergrammer2 to explore high-dimensional datasets.

Useful bioinformatic scripts

WebLogo 3: Sequence Logos redrawn

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

VirNet: A deep attention model for viral reads identification

An open-access bioinformatics text

De novo assembly based variant calling pipeline for Illumina short reads

Unsupervised domain adaptation method for relation extraction

d3js box plot plugin

Aim to be the bioinformatics repository with more and newer packages

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

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

A Python platform for Structural Bioinformatics

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

Mulled - Automatized Containerized Software Repository

Introduction to the Unix Shell for biologists

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

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Compute N50/NG50 and auN/auNG

🎤 Lyrics/associated NLP data for Billboard's Top 100, 1950-2015.

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

An implementation of Conway's Game of Life in Elixir

WebGL Heatmap Viewer for Big Data and Bioinformatics

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

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

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

利用台北市政府開放的建築使用執照資料，製作台北市屋齡地圖

Mapping-Assisted Targeted-Assembly for Metagenomics

🎯 Human transcription factor target genes.

Curated list of bioinformatics formats and publications

简单的可视化湖州通话数据 假设数据量很大，没法用浏览器直接绘制热力图，把绘制热力图这一步骤放到线下计算分析。使用Apache Spark并行计算数据之后，再使用Apache Spark绘制热力图，然后用leafletjs加载OpenStreetMap图层和热力图图层，以达到良好的交互效果。现在使用Apache Spark实现绘制，可能是Apache Spark不擅长这方面的计算或者是我没有设计好算法，并行计算的速度比不上单机计算。Apache Spark绘制热力图和计算代码在这 https://github.com/yuanzhaokang/ParallelizeHeatmap.git .

Read and write FASTQ and FASTA efficiently from Python

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

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

The Microbiome Interpretable Temporal Rule Engine

A library to build and execute typed scientific workflows

exploratory and interactive microbiome analyses based on heatmaps

[NOT MAINTAINED] A D3js library for drawing polytopes, angles, coordinates, geometries and more.

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

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

The uncompromising Snakemake code formatter