Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "microbiome" keyword
nmdc-schema 10.3.0
Schema resources for the National Microbiome Data Collaborative (NMDC)73 versions - Latest release: 2 days ago - 3.16 thousand downloads last month - 26 stars on GitHub - 4 maintainers
amon-bio 1.0.4
Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins f...5 versions - Latest release: 3 months ago - 51 downloads last month - 17 stars on GitHub - 2 maintainers
dyspyosis 0.1.0
Calculate dysbiosis scores using Python3 versions - Latest release: 4 days ago - 125 downloads last month - 1 stars on GitHub - 1 maintainer
anadama2 0.10.0
AnADAMA2: Another Automated Data Analysis Management Application 221 versions - Latest release: over 1 year ago - 1 dependent package - 3 dependent repositories - 121 downloads last month - 1 maintainer
Top 9.2% on pypi.org
3 versions - Latest release: almost 2 years ago - 2 dependent packages - 4 dependent repositories - 75 downloads last month - 26 stars on GitHub - 1 maintainer
calour 2019.5.1
CALOUR: exploratory and interactive microbiome analyses based on heatmap3 versions - Latest release: almost 2 years ago - 2 dependent packages - 4 dependent repositories - 75 downloads last month - 26 stars on GitHub - 1 maintainer
q2sra 1.0.0
Fetch, process, analyze, and aggregate microbiome sequencing data with SRA Toolkit and QIIME2.1 version - Latest release: about 2 months ago - 52 downloads last month - 1 stars on GitHub - 1 maintainer
parathaa 0.1.0
PARATHAA: Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assig...1 version - Latest release: 5 months ago - 20 downloads last month - 1 stars on GitHub - 1 maintainer
mimic-da 1.0.0
16 versions - Latest release: about 1 month ago - 123 downloads last month - 1 stars on GitHub - 2 maintainersmicroberx 0.2.6
MicrobeRX is A tool for enzymatic reaction-based metabolite prediction in the gut microbiome.10 versions - Latest release: 4 months ago - 31 downloads last month - 7 stars on GitHub - 1 maintainer
pymgpipe 0.16.10
Community level microbiome metabolic modeling in Python5 versions - Latest release: 10 months ago - 42 downloads last month - 6 stars on GitHub - 1 maintainer
metasbt 0.1.2
A scalable framework for automatically indexing microbial genomes and accurately characterizing m...3 versions - Latest release: about 1 year ago - 4 downloads last month - 0 stars on GitHub - 1 maintainer
xlassify 1.0.0
An alignment-free deep-learning model trained to classify human gut bacteria2 versions - Latest release: about 2 years ago - 1 dependent repositories - 8 downloads last month - 1 maintainer
woltka 0.1.6
versatile meta-omic data classifier5 versions - Latest release: 3 months ago - 1 dependent repositories - 71 downloads last month - 64 stars on GitHub - 1 maintainer
vica 0.1.5
find highly divergent DNA and RNA viruses in microbiomes3 versions - Latest release: about 6 years ago - 1 dependent repositories - 16 downloads last month - 5 stars on GitHub - 1 maintainer
ubiome 0.6.5
uBiome core taxonomy library7 versions - Latest release: almost 8 years ago - 2 dependent repositories - 31 downloads last month - 66 stars on GitHub - 1 maintainer
tasccoda 0.1.3
Tree-aggregated compositional analysis for high-throughput sequencing data4 versions - Latest release: over 1 year ago - 1 dependent repositories - 28 downloads last month - 8 stars on GitHub - 1 maintainer
superfocus 1.4.1
SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data8 versions - Latest release: over 2 years ago - 1 dependent repositories - 43 downloads last month - 19 stars on GitHub - 2 maintainers
sourcepredict 0.5
Classification and prediction of the origin of metagenomic samples1 version - Latest release: about 4 years ago - 1 dependent repositories - 15 downloads last month - 5 stars on GitHub - 1 maintainer
shortbred 0.9.5
ShortBRED: a system for profiling protein families of interest at very high specificity in shotgu...1 version - Latest release: almost 4 years ago - 1 dependent repositories - 8 downloads last month - 1 maintainer
qurro 0.8.0
Visualizes differentially ranked features and log-ratios of their sample abundances10 versions - Latest release: over 1 year ago - 1 dependent repositories - 94 downloads last month - 30 stars on GitHub - 1 maintainer
qupid 0.1.0
Case-control matching for microbiome data.3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 31 downloads last month - 11 stars on GitHub - 1 maintainer
qiita-spots 0.2.0
Qiita: Spot Patterns3 versions - Latest release: over 8 years ago - 12 dependent repositories - 18 downloads last month - 119 stars on GitHub - 1 maintainer
Top 8.0% on pypi.org
4 versions - Latest release: almost 9 years ago - 8 dependent repositories - 133 downloads last month - 1 maintainer
qiime 1.9.1
Quantitative Insights Into Microbial Ecology4 versions - Latest release: almost 9 years ago - 8 dependent repositories - 133 downloads last month - 1 maintainer
qbiome 0.0.67
Analyzing microbiome abundance data to infer deep structures58 versions - Latest release: about 1 month ago - 1 dependent repositories - 545 downloads last month - 0 stars on GitHub - 2 maintainers
q2-micom 0.14.0
QIIME 2 plugin for metabolic modeling of microbial communities.20 versions - Latest release: 24 days ago - 1 dependent repositories - 339 downloads last month - 10 stars on GitHub - 1 maintainer
q2-dbbact 1.5.0
A qiime2 (https://qiime2.org/) plugin for dbBact (http://dbbact.org) annotations of microbiome ex...8 versions - Latest release: about 1 year ago - 1 dependent repositories - 76 downloads last month - 1 stars on GitHub - 1 maintainer
ocms-16s 0.0.2
OCMS_16S : Oxford Centre for Microbiome Studies pipelines for 16S amplicon sequencing analysis2 versions - Latest release: over 2 years ago - 1 dependent repositories - 9 downloads last month - 2 stars on GitHub - 1 maintainer
nmdc 0.2.1
Command line toolbox of NMDC (https://microbiomedata.org/)1 version - Latest release: over 3 years ago - 1 dependent repositories - 11 downloads last month - 2 maintainers
mitre 1.0b1
Microbiome Interpretable Temporal Rule Engine6 versions - Latest release: over 5 years ago - 1 dependent repositories - 68 downloads last month - 45 stars on GitHub - 1 maintainer
misdeed 1.0.3
Microbiome Synthetic Data Engine for Experimental Design4 versions - Latest release: 8 months ago - 1 dependent repositories - 38 downloads last month - 5 stars on GitHub - 1 maintainer
microbiome-toolbox 1.0.2
Microbiome Toolbox12 versions - Latest release: about 2 years ago - 1 dependent repositories - 84 downloads last month - 8 stars on GitHub - 1 maintainer
micom 0.35.0
Microbial community modeling based on cobrapy.106 versions - Latest release: 28 days ago - 1 dependent package - 1 dependent repositories - 805 downloads last month - 77 stars on GitHub - 1 maintainer
metawibele 0.4.7
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome10 versions - Latest release: 8 months ago - 1 dependent repositories - 52 downloads last month - 18 stars on GitHub - 1 maintainer
metagenomics-focus 1.8
FOCUS: An Agile Profiler for Metagenomic Data4 versions - Latest release: over 2 years ago - 1 dependent repositories - 51 downloads last month - 7 stars on GitHub - 2 maintainers
humann2 2.8.2
HUMAnN2: The HMP Unified Metabolic Analysis Network 225 versions - Latest release: about 4 years ago - 6 dependent repositories - 132 downloads last month - 1 maintainer
humann 3.6.1
HUMAnN: The HMP Unified Metabolic Analysis Network, version 315 versions - Latest release: about 1 year ago - 1 dependent repositories - 584 downloads last month - 1 maintainer
hiorco 1.0.0
Higher-Order Co-occurrence1 version - Latest release: over 4 years ago - 1 dependent repositories - 27 downloads last month - 9 stars on GitHub - 1 maintainer
gtnet 0.1.0
A package for running Genome Taxonomy Network predictions8 versions - Latest release: 2 months ago - 1 dependent repositories - 81 downloads last month - 1 stars on GitHub - 2 maintainers
gemelli 0.0.10
Robust Aitchison Tensor Decomposition for sparse count data10 versions - Latest release: 4 months ago - 1 dependent repositories - 198 downloads last month - 63 stars on GitHub - 1 maintainer
famli 1.2
Functional Analysis of Metagenomes by Likelihood Inferrence3 versions - Latest release: about 4 years ago - 1 dependent repositories - 33 downloads last month - 16 stars on GitHub - 1 maintainer
ezcalour 1.12.4
EZCalour: GUI frontend tool for Calour microbiome analysis software2 versions - Latest release: over 3 years ago - 1 dependent repositories - 19 downloads last month - 1 stars on GitHub - 1 maintainer
empress 1.2.0
Fast and scalable phylogenetic tree viewer for multi-omic data analysis5 versions - Latest release: almost 3 years ago - 1 dependent repositories - 200 downloads last month - 44 stars on GitHub - 2 maintainers
Top 7.9% on pypi.org
34 versions - Latest release: 10 months ago - 8 dependent repositories - 190 downloads last month - 53 stars on GitHub - 1 maintainer
emperor 1.0.4
Emperor34 versions - Latest release: 10 months ago - 8 dependent repositories - 190 downloads last month - 53 stars on GitHub - 1 maintainer
dram-bio 1.5.0
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of functio...29 versions - Latest release: 5 months ago - 1 dependent repositories - 413 downloads last month - 223 stars on GitHub - 3 maintainers
dbbact-calour 1.15.0
dbbact-calour is a Calour (https://github.com/biocore/calour) interface for dbBact (dbbact.org)14 versions - Latest release: about 1 year ago - 1 dependent package - 2 dependent repositories - 150 downloads last month - 1 stars on GitHub - 1 maintainer
yms 1.2.11
YOLO Microbiome Analysis System52 versions - Latest release: 12 days ago - 618 downloads last month - 5 stars on GitHub - 2 maintainers
birdman 0.2.0
Framework for differential microbiome abundance using Bayesian inference6 versions - Latest release: 7 months ago - 88 downloads last month - 22 stars on GitHub - 1 maintainer
biobakery-workflows 0.15.1
bioBakery workflows: A collection of meta'omic analysis workflows24 versions - Latest release: almost 4 years ago - 101 downloads last month - 1 maintainer
amptk 1.6.0
AMPtk: amplicon tool kit11 versions - Latest release: 6 months ago - 1 dependent repositories - 65 downloads last month - 35 stars on GitHub - 1 maintainer
xebec 0.5.1
Snakemake pipeline for microbiome diversity effect size benchmarking.2 versions - Latest release: almost 2 years ago - 1 dependent repositories - 22 downloads last month - 5 stars on GitHub - 1 maintainer
kneaddata 0.12.0
13 versions - Latest release: over 1 year ago - 1 dependent repositories - 204 downloads last month - 1 maintainerhdmf-ml 0.0.1
A package for using the HDMF-ML schema1 version - Latest release: over 1 year ago - 20 downloads last month - 1 stars on GitHub - 1 maintainer
mifaser 1.60
a python package for super-fast and accurate annotation of molecular functionality using read dat...3 versions - Latest release: about 4 years ago - 1 dependent repositories - 37 downloads last month - 1 maintainer
qiime-tools 1.1.2
Useful additions to the QIIME analysis pipeline including tools for data visualization and cluste...3 versions - Latest release: over 9 years ago - 3 dependent repositories - 41 downloads last month - 12 stars on GitHub - 1 maintainer
locate-model 0.0.3
This code is attached to the paper "Microbiome-metabolome interactions predict host phenotype".3 versions - Latest release: over 1 year ago - 29 downloads last month - 3 stars on GitHub - 1 maintainer
miscoto 3.2.0
Microbiome Screening and COmmunity selection using TOpology30 versions - Latest release: 3 months ago - 1 dependent package - 2 dependent repositories - 240 downloads last month - 6 stars on GitHub - 2 maintainers
Top 8.5% on pypi.org
10 versions - Latest release: over 1 year ago - 1 dependent package - 4 dependent repositories - 272 downloads last month - 43 stars on GitHub - 1 maintainer
redbiom 0.3.9
Sample search by metadata and features10 versions - Latest release: over 1 year ago - 1 dependent package - 4 dependent repositories - 272 downloads last month - 43 stars on GitHub - 1 maintainer
panphlan 1.3
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *i...2 versions - Latest release: almost 4 years ago - 1 dependent repositories - 20 downloads last month - 39 stars on GitHub - 1 maintainer
qadabra 0.3.0
Differential abundance workflow for microbiome data2 versions - Latest release: 4 months ago - 27 downloads last month - 14 stars on GitHub - 1 maintainer
micone 0.15.0
The Microbial Co-occurrence Network Explorer28 versions - Latest release: 8 months ago - 1 dependent repositories - 169 downloads last month - 18 stars on GitHub - 1 maintainer
phylotoast 1.3.0
Tools for phylogenetic data analysis including visualization and cluster-computing support.1 version - Latest release: about 8 years ago - 2 dependent repositories - 18 downloads last month - 12 stars on GitHub - 1 maintainer
Related Keywords
bioinformatics
35
python
13
microbiology
10
metagenomics
9
microbial
8
metagenomic
7
microbiome-analysis
6
qiime
6
metatranscriptomic
5
machine-learning
5
visualization
5
analysis
4
anadama2
4
qiime2
4
cross-platform
4
computational-biology
4
metabolic-models
4
pipeline
3
metabolism
3
humann
3
genomics
3
modeling
3
community
2
hacktoberfest
2
tensorflow
2
metagenome
2
metagenome-assembled-genomes
2
systems-biology
2
dbbact
2
cobra
2
slurm
2
phylogenetics
2
pbs
2
microbial-genomics
2
hpc
2
16s
2
16S
2
microbial ecology
2
QIIME
2
snakemake
2
ordination
2
reproducible-research
2
open-science
2
open-source
2
data-format
2
open-data
2
microbial-taxonomy
2
data-analysis
2
bayesian-inference
2
database
2
metabolite
2
heatmap
2
workflow
2
neural-network
2
NMDC
2
taxonomic-classification
1
compositional-data-analysis
1
ctf
1
joint-rpca
1
rclr
1
rpca
1
tempted
1
science
1
GUI
1
biplot
1
samples
1
phylogeny
1
tree-plot
1
biplots
1
emperor
1
annotation
1
viral-genomics
1
genome
1
tools
1
focus_app
1
identify-organisms
1
kmer
1
metagenomes
1
package
1
humann2
1
hiorco
1
cooccurrence
1
microbial-communities
1
deep-learning
1
data-science
1
omics-data-integration
1
metabolome
1
transcriptomics
1
standards
1
metagenomic-analysis
1
metagenomic-classification
1
mixs
1
microbiomedata
1
metabolomics
1
linkml
1
fair-data
1
ecoinformatics
1
metadata
1
schema
1
ML
1