642 Open source projects that are alternatives of or similar to mitre

Data-driven Network-based Bayesian Inference of Drivers

Syntax highlighting for computational biology

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…

The sources of the openSNP website

Infer the gender of an individual based on their name.

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

An open-access bioinformatics text

Next generation sequencing reads de novo assembler.

The Ensembl Compara Perl API and SQL schema

R package for analyzing single-cell RNA-seq data

MMseqs2 app to run on your workstation or servers

Package for fetching metadata and downloading data from SRA/ENA/GEO

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

parallel fastq-dump wrapper

Unsupervised domain adaptation method for relation extraction

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

Fitness landscape exploration sandbox for biological sequence design.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Qiita - A multi-omics databasing effort

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

A fast and scalable phylogenetic tree viewer for microbiome data analysis

🎓 Uni-Bonn Decision Analysis graduate course, lectures and materials

nim wrapper for htslib for parsing genomics data files

Fast and flexible ORF finder

Simple simulation of single-cell RNA sequencing data

A Go package for engineering organisms.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

No description or website provided.

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

Deodorant: Solving the problems of Bayesian Optimization

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Bystro genetic analysis (annotation, filtering, statistics)

Single cell perturbation prediction

Material for a workshop on Bayesian stats with R

Application for making ENCODE Blacklists

Mapping-Assisted Targeted-Assembly for Metagenomics

dna2vec: Consistent vector representations of variable-length k-mers

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

APBS - software for biomolecular electrostatics and solvation

Estimating effective elastic thickness of the lithosphere

An efficient FASTQ manipulation suite

pyQms, generalized, fast and accurate mass spectrometry data quantification

UGENE is free open-source cross-platform bioinformatics software

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

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Implementations of single and multi-ellipsoid nested sampling

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

Method to optimally select samples for validation and resequencing

A Practical and Efficient NCBI Taxonomy Toolkit

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

A model-based visualization method for microbiome data

Code and Data to accompany "Dilated Convolutions for Modeling Long-Distance Genomic Dependencies", presented at the ICML 2017 Workshop on Computational Biology

DOM Text Based Multiple Sequence Alignment Library

A simplified pipeline for ctDNA sequencing data analysis

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.

Schloss Lab Tools for Reproducible Microbiome Research 💩

VirNet: A deep attention model for viral reads identification

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