499 Open source projects that are alternatives of or similar to Khmer

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

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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.

16,432 Free Yara rules created by

Sample search by metadata and features

Biostar Q&A

WebLogo 3: Sequence Logos redrawn

Interactive network visualization in Python and Dash, powered by Cytoscape.js

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

A cross-platform command-line tool for executing jobs in parallel

The Microbiome Interpretable Temporal Rule Engine

A simplified pipeline for ctDNA sequencing data analysis

List of Computer Science courses with video lectures.

Phylogenetic trees in Julia

🎯 Bloom filters for C++11

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.

Tools for working with SAM/BAM data

De novo assembly based variant calling pipeline for Illumina short reads

Modular and universal bioinformatics

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

The Chemistry Development Kit

Build and maintain multiple custom conda environments all in once place.

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

Earl Grey: A fully automated TE curation and annotation pipeline

An open source platform for managing and analyzing biomedical big data

推荐算法、相似度算法、布隆过滤器、均值算法、一致性Hash、数据结构、leetcode练习

Unix, R and python tools for genomics and data science

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Structural variant and indel caller for mapped sequencing data

Predict plasmids from uncorrected long read data

A fast and sensitive gapped read aligner

Examples using Clustergrammer2 to explore high-dimensional datasets.

COBRApy is a package for constraint-based modeling of metabolic networks.

VirNet: A deep attention model for viral reads identification

Versatile open-source tool for microbiome analysis

🚦 Run Picard on BAM files and collate 90 metrics into one file.

A high-performance, Pythonic language for bioinformatics

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Plant image analysis using OpenCV

Introduction to the Unix Shell for biologists

A React web application to query and share any PostgreSQL database.

Scripts to download genomes from the NCBI FTP servers

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

MMseqs2: ultra fast and sensitive search and clustering suite

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

annotate a VCF with other VCFs/BEDs/tabixed files

Mapping-Assisted Targeted-Assembly for Metagenomics

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

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Ultra-fast and memory-efficient (meta-)genome assembler

A simple but fast bloomfilter written in Python

A library to build and execute typed scientific workflows

exploratory and interactive microbiome analyses based on heatmaps

2021年最新总结 500个常用数据结构，算法，算法导论，面试常用，大厂高级工程师整理总结

Fast motif matching in R

Bloomfilter written in Golang, includes rotation and RPC

Workflow Description Language - Specification and Implementations