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biocore

biocore

Geek Repo

Collaboratively developed bioinformatics software.

Location:Cyberspace

Home Page:http://biocore.github.io/

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biocore's repositories

deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.

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biom-format

The Biological Observation Matrix (BIOM) Format Project

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tcga

Microbial analysis in TCGA data

Language:Jupyter NotebookLicense:BSD-3-ClauseStargazers:88Issues:10Issues:10

gemelli

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

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emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

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redbiom

Sample search by metadata and features

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unifrac

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q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

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calour

exploratory and interactive microbiome analyses based on heatmaps

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q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database

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BIRDMAn

Bayesian Inferential Regression for Differential Microbiome Analysis

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tax2tree

Automated taxonomy decoration onto a tree

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evident

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qadabra

Snakemake workflow for comparison of differential abundance ranks

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greengenes2

Processing support for Greengenes2

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metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing

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pynast

Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests

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zebra_filter

Filtering out false taxonomic hits from shotgun sequencing based on genome coverage

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microsetta-private-api

A private microservice to support The Microsetta Initiative

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american-gut-web

The website for the American Gut Project participant portal

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improved-octo-waddle

Balanced parentheses succinct data structure in Python

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micov

Aggregate genome coverage

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mg-scripts

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal

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microsetta-interface

The Microsetta participant facing user interface

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q2-katharoseq

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unifrac-binaries

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microsetta-admin

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absquant

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microsetta-processing

Processing scripts for The Microsetta Initiative

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mustached-octo-ironman

Easy dispatched compute in a Tornado environment

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