@biocore
Guthub

biocore

Twitter logo Share LinkedIn logo Share Facebook logo Share

Top repositories

1

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
Python
781
star
2

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Python
285
star
3

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool
C++
169
star
4

emp

Code repository of the Earth Microbiome Project.
Jupyter Notebook
154
star
5

mmvec

Neural networks for microbe-metabolite interaction analysis
Python
117
star
6

American-Gut

American Gut open-access data and IPython notebooks
Jupyter Notebook
107
star
7

biom-format

The Biological Observation Matrix (BIOM) Format Project
Python
92
star
8

deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
Python
91
star
9

tcga

Microbial analysis in TCGA data
Jupyter Notebook
88
star
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.
Python
67
star
11

songbird

Vanilla regression methods for microbiome differential abundance analysis
Python
56
star
12

gneiss

compositional data analysis toolbox
Jupyter Notebook
55
star
13

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets
JavaScript
52
star
14

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis
JavaScript
45
star
15

redbiom

Sample search by metadata and features
Python
44
star
16

unifrac

Python
37
star
17

scikit-bio-cookbook

Recipes for bioinformatics analyses with scikit-bio
Jupyter Notebook
36
star
18

DEICODE

Robust Aitchison PCA from sparse count data
JavaScript
33
star
19

q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Python
31
star
20

qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
JavaScript
31
star
21

calour

exploratory and interactive microbiome analyses based on heatmaps
Python
27
star
22

q2-greengenes2

A QIIME 2 plugin for interaction with the Greengenes2 database
Python
26
star
23

wol

Reference Phylogeny for Bacterial and Archaeal Genomes
Jupyter Notebook
24
star
24

BIRDMAn

Bayesian Inferential Regression for Differential Microbiome Analysis
Python
22
star
25

Platypus-Conquistador

Confirming specific taxonomic groups within your samples.
Python
19
star
26

micronota

annotation pipeline for microbial genomes and metagenomes
Python
18
star
27

tax2tree

Automated taxonomy decoration onto a tree
Python
14
star
28

evident

Python
14
star
29

qadabra

Snakemake workflow for comparison of differential abundance ranks
Python
13
star
30

oecophylla

shotgun pipeline
Python
11
star
31

horizomer

Workflow for detecting genome-wide horizontal gene transfers
Python
11
star
32

greengenes2

Processing support for Greengenes2
Python
11
star
33

pyqi

Tools for developing and testing command line interfaces in Python.
Python
9
star
34

burrito

Python framework for controlling command-line applications.
Python
8
star
35

pynast

Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests
Python
8
star
36

metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
Python
8
star
37

my-microbes

A set of tools for delivering personal microbiome results to individuals participating in microbiome sequencing studies.
Python
7
star
38

zebra_filter

Filtering out false taxonomic hits from shotgun sequencing based on genome coverage
Python
7
star
39

burrito-fillings

Application controllers for command line bioinformatics applications
Python
7
star
40

Evident-initial-demo

Elucidating sampling effort for microbial analysis studies
JavaScript
7
star
41

mds-approximations

Multidimensional scaling algorithms for microbiology-ecology datasets.
Python
6
star
42

microsetta-private-api

A private microservice to support The Microsetta Initiative
Python
6
star
43

conda-recipes

conda recipes for bioinformatic tools like blast+, infernal, etc.
Python
6
star
44

american-gut-web

The website for the American Gut Project participant portal
Python
5
star
45

qiime-default-reference

Default reference data files for use with QIIME.
Python
4
star
46

scikit-bio-rfcs

Request For Comments (RFCs) for scikit-bio.
4
star
47

labadmin

Administration website for the Knight Lab
Python
4
star
48

q2-umap

Applying umap to microbiome data via QIIME2
Python
4
star
49

improved-octo-waddle

Balanced parentheses succinct data structure in Python
Jupyter Notebook
4
star
50

dsFDR

descrete False Discovery Rate method
Python
3
star
51

SitePainter

A tool for exploring biogeographical patterns
JavaScript
3
star
52

bayestime

Jupyter Notebook
3
star
53

genome-subsampler

Statistical and empirical subsampling of reference genomes
Jupyter Notebook
3
star
54

micov

Aggregate genome coverage
Python
3
star
55

cmi-workshops

2
star
56

taxster

taxster: assigning taxonomy to organisms you've never even heard of
Python
2
star
57

PipeClust

MPI-based sequence clusterer
C
2
star
58

microsetta-public-api

A public microservice to support The Microsetta Initiative
Python
2
star
59

LabControl

lab manager for plate maps and sequence flows
Python
2
star
60

american-gut-rest

RESTful interface into the American Gut data
Python
2
star
61

unifrac-binaries

C++
1
star
62

biocore.github.io

CSS
1
star
63

q2-ili

QIIME2 plugin for `ili
Python
1
star
64

q2-katharoseq

Python
1
star
65

microsetta-interface

The Microsetta participant facing user interface
Jinja
1
star
66

qiime-workshops

Materials for biocore organized workshops
Jupyter Notebook
1
star
67

microprot

structural annotation pipeline for microbial genomes and metagenomes
Python
1
star
68

mg-scripts

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal
Python
1
star
69

sage-emperor

Emperor implementation in the SAGE2 framework
JavaScript
1
star
70

q2-mislabeled

A QIIME 2 plugin for assessing sample mislabeling and contamination
Python
1
star
71

q2-american-gut

A QIIME2 plugin for working with and processing American Gut data
Python
1
star
72

basespace-qiime

QIIME's BaseSpace App
HTML
1
star