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biocore

60 indexed repositories · View on GitHub

emp
Code repository of the Earth Microbiome Project.

Jupyter Notebook · 169 stars
American-Gut
American Gut open-access data and IPython notebooks

Jupyter Notebook · 133 stars
mmvec
Neural networks for microbe-metabolite interaction analysis

Python · 133 stars
deblur
Deblur is a greedy deconvolution algorithm based on known read error profiles.

Python · 101 stars
biom-format
The Biological Observation Matrix (BIOM) Format Project

Python · 98 stars
tcga
Microbial analysis in TCGA data

Jupyter Notebook · 94 stars
gemelli
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TE...

Python · 92 stars
gneiss
compositional data analysis toolbox

Jupyter Notebook · 63 stars
songbird
Vanilla regression methods for microbiome differential abundance analysis

Python · 62 stars
empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis

JavaScript · 56 stars
emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets

JavaScript · 54 stars
redbiom
Sample search by metadata and features

Python · 49 stars
unifrac

Python · 43 stars
DEICODE
Robust Aitchison PCA from sparse count data

JavaScript · 37 stars
q2-greengenes2
A QIIME 2 plugin for interaction with the Greengenes2 database

Python · 35 stars
qurro
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

JavaScript · 35 stars
q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Python · 31 stars
calour
exploratory and interactive microbiome analyses based on heatmaps

Python · 27 stars
BIRDMAn
Bayesian Inferential Regression for Differential Microbiome Analysis

Python · 25 stars
Platypus-Conquistador
Confirming specific taxonomic groups within your samples.

Python · 19 stars
40 more repositories live on View on GitHub

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1420 open issues indexed

Add install notes Open

biocore/PipeClust#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Create HDF5 output files Open

biocore/PipeClust#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Expand # of colors that can be used in color gradients Open

biocore/SitePainter#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Automatically print all plots Open

biocore/SitePainter#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Setup a server to run the latest version of SitePainter Open

biocore/SitePainter#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use latest version as stable version Open

biocore/SitePainter#11 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Change repo name to sitepainter (all lowercase) Open

question

biocore/SitePainter#12 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Ad travis to SitePainter Open

enhancement

biocore/SitePainter#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Harden regex on sample IDs Open

biocore/american-gut-rest#10 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
A developer should be able to get taxonomy information Open

biocore/american-gut-rest#11 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
A user should be able to obtain their alpha diversity results Open

biocore/american-gut-rest#13 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Users have to download the app results to access the visualizations Open

bug qiime-visualizations

biocore/basespace-qiime#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
QIIME Downstream should be able to take more than one app result Open

enhancement qiime-visualizations

biocore/basespace-qiime#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
rarefaction curve cannot show in browser Open

bug

biocore/basespace-qiime#5 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
four samples preprocessing fails Open

biocore/basespace-qiime#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add parameter to track number of times a lot, primer plate, etc is used and a way to warn if too many uses Open

feature request scope:large

biocore/LabControl#31 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Highlight cells per study Open

feature request scope:medium

biocore/LabControl#52 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Implement repooling functionality Open

feature request scope:large

biocore/LabControl#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
change license Open

biocore/taxster#1 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Create an interface that, given a plate, provides its ancestry and descendency Open

feature request priority:medium scope:large

biocore/LabControl#77 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Comments from call Open

biocore/taxster#3 · 14 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Refactor backend to rename 16S to amplicon Open

code refactor scope:medium

biocore/LabControl#91 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add comment box in gDNA plate extraction Open

feature request scope:medium

biocore/LabControl#128 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Implement unit tests for javascript functionality Open

code refactor priority:high scope:large

biocore/LabControl#171 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Which application controllers do we want to maintain? Open

biocore/burrito-fillings#1 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Stress test the software Open

enhancement priority:high scope:large

biocore/LabControl#173 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
fastq_join.py app controller does not have tests Open

biocore/burrito-fillings#2 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
seqprep.py app controller does not have tests Open

biocore/burrito-fillings#3 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Idea: Is there any way to integrate a biosafetly level warning button that goes away once the samples are extracted? Open

feature request scope:unknown

biocore/LabControl#179 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
rdp_classifier.py app controler may not include complete tests Open

biocore/burrito-fillings#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
export all plate maps from a single study to a tsv/excel file Open

feature request scope:unknown

biocore/LabControl#190 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
mothur.py app controller may not be completely tested Open

biocore/burrito-fillings#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Ensure that data duplication by "contents" field in sample_composition is acceptable Open

code refactor priority:high scope:large

biocore/LabControl#220 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
brokit-wrapped applications that are not currently installed in the QIIME VM Open

biocore/burrito-fillings#20 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add ENV_package to sample sheet Open

feature request priority:high scope:medium

biocore/LabControl#227 · 22 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
missing tmp dir in get_clusters_from_fasta_filepath function from uclust Open

biocore/burrito-fillings#21 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make a more generalized 'upstream' connector in composition objects/tables? Open

code refactor scope:large

biocore/LabControl#234 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow for `--usearch_local` in usearch 6.1 Open

biocore/burrito-fillings#22 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Change sample sheet Sample_ID and Sample_Name to use actual sample id instead of sample "content"? Open

enhancement scope:small wontfix

biocore/LabControl#237 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
update brokit license information to indicate that it's actually GPL Open

biocore/burrito-fillings#27 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Vienna package controller Open

biocore/burrito-fillings#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add comments to multiple wells based on selection Open

feature request scope:large

biocore/LabControl#244 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
brokit.get_clusters_from_fasta_filepath failing to remove output files Open

biocore/burrito-fillings#31 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add tooltips to pooling interface to explain parameter values Open

feature request front-end priority:medium scope:small

biocore/LabControl#249 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Change to the numpy doc standard for sortmerna + sumaclust api's Open

biocore/burrito-fillings#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
for gDNA plate compression, add diagram to output Open

feature request scope:medium

biocore/LabControl#252 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
add import of cogent aligner for access in QIIME Open

biocore/burrito-fillings#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Prevent creation of sequencing runs without all lanes filled Open

feature request scope:small wontfix

biocore/LabControl#261 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
usearch de novo (no chimera checking) gives incorrect results Open

biocore/burrito-fillings#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consolidate "components" attribute logic in PoolingProcess and PoolComposition Open

code refactor priority:low scope:small

biocore/LabControl#265 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

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