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

exploratory and interactive microbiome analyses based on heatmaps

Sample search by metadata and features

A web interface for exploring PyMC3 traces

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

A library to build and execute typed scientific workflows

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

Earl Grey: A fully automated TE curation and annotation pipeline

Introduction to the Unix Shell for biologists

Jupyter notebooks with examples of statistical methods and analyses using R.

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

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

De novo assembly based variant calling pipeline for Illumina short reads

A fast 23andMe genome text file parser, now superseded by arv

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

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

Particle filtering and sequential parameter inference in Python

Phylogenetic trees in Julia

Material for AMLD 2020 workshop "Bayesian Inference: embracing uncertainty"

Efficient, lightweight variational inference and approximation bounds

Forecasting 🇫🇷 elections with Bayesian statistics 🥳

Fast motif matching in R

Sleek implementations of the ZigZag, Boomerang and other assorted piecewise deterministic Markov processes for Markov Chain Monte Carlo including Sticky PDMPs for variable selection

Code for "Functional variational Bayesian neural networks" (https://arxiv.org/abs/1903.05779)

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

Curated list of bioinformatics formats and publications

Full Bayesian Inference for Hidden Markov Models

micca - MICrobial Community Analysis

R package for microbiome biomarker discovery

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

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…

MMseqs2 app to run on your workstation or servers

Qiita - A multi-omics databasing effort

No description or website provided.

Mapping-Assisted Targeted-Assembly for Metagenomics

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

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

📊 Identify cell types and pathways affected by genetic risk loci.

nessai: Nested Sampling with Artificial Intelligence

React rerelease of MSAViewer

No description or website provided.

Predict plasmids from uncorrected long read data

A curated list of awesome bioinformatics software.

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

Compare different differential abundance and expression methods

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

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

Project metadata manager for PEPs in Python

Helper functions for brmsfit objects (DEPRECATED)

The Ontology for Biomedical Investigations

Genotyping of segregating mobile elements insertions

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.

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

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

Examples using Clustergrammer2 to explore high-dimensional datasets.

Read DNA sequences from colourful Microsoft Word documents

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.

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.