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
famli 1.2
Functional Analysis of Metagenomes by Likelihood Inferrence3 versions - Latest release: over 4 years ago - 1 dependent repositories - 27 downloads last month - 16 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
34 versions - Latest release: 11 months ago - 8 dependent repositories - 153 downloads last month - 52 stars on GitHub - 1 maintainer
emperor 1.0.4
Emperor34 versions - Latest release: 11 months ago - 8 dependent repositories - 153 downloads last month - 52 stars on GitHub - 1 maintainer
gtnet 0.1.0
A package for running Genome Taxonomy Network predictions8 versions - Latest release: 3 months ago - 1 dependent repositories - 65 downloads last month - 1 stars on GitHub - 2 maintainers
sourcepredict 0.5
Classification and prediction of the origin of metagenomic samples1 version - Latest release: over 4 years ago - 1 dependent repositories - 13 downloads last month - 5 stars on GitHub - 1 maintainer
hdmf-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
gemelli 0.0.10
Robust Aitchison Tensor Decomposition for sparse count data10 versions - Latest release: 5 months ago - 1 dependent repositories - 143 downloads last month - 66 stars on GitHub - 1 maintainer
nmdc-schema 10.3.0
Schema resources for the National Microbiome Data Collaborative (NMDC)85 versions - Latest release: 26 days ago - 1.64 thousand downloads last month - 26 stars on GitHub - 4 maintainers
qupid 0.1.0
Case-control matching for microbiome data.3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 11 downloads last month - 11 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 - 19 downloads last month - 1 maintainer
microberx 0.2.6
MicrobeRX is A tool for enzymatic reaction-based metabolite prediction in the gut microbiome.12 versions - Latest release: 4 months ago - 76 downloads last month - 7 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 - 243 downloads last month - 236 stars on GitHub - 3 maintainers
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
qbiome 0.0.67
Analyzing microbiome abundance data to infer deep structures58 versions - Latest release: 2 months ago - 1 dependent repositories - 131 downloads last month - 0 stars on GitHub - 2 maintainers
parathaa 0.1.0
PARATHAA: Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assig...1 version - Latest release: 6 months ago - 14 downloads last month - 1 stars on GitHub - 1 maintainer
Top 8.0% on pypi.org
4 versions - Latest release: about 9 years ago - 8 dependent repositories - 120 downloads last month - 1 maintainer
qiime 1.9.1
Quantitative Insights Into Microbial Ecology4 versions - Latest release: about 9 years ago - 8 dependent repositories - 120 downloads last month - 1 maintainer
dyspyosis 0.1.0
Calculate dysbiosis scores using Python3 versions - Latest release: 27 days ago - 262 downloads last month - 1 stars on GitHub - 1 maintainer
phylotoast 1.3.0
Tools for phylogenetic data analysis including visualization and cluster-computing support.1 version - Latest release: over 8 years ago - 2 dependent repositories - 15 downloads last month - 12 stars on GitHub - 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 - 14 downloads last month - 12 stars on GitHub - 1 maintainer
yms 1.2.11
YOLO Microbiome Analysis System53 versions - Latest release: about 1 month ago - 618 downloads last month - 5 stars on GitHub - 2 maintainers
mimic-da 1.0.0
17 versions - Latest release: 2 months ago - 123 downloads last month - 1 stars on GitHub - 2 maintainersqurro 0.8.0
Visualizes differentially ranked features and log-ratios of their sample abundances10 versions - Latest release: over 1 year ago - 1 dependent repositories - 57 downloads last month - 30 stars on GitHub - 1 maintainer
hiorco 1.0.0
Higher-Order Co-occurrence1 version - Latest release: over 4 years ago - 1 dependent repositories - 10 downloads last month - 9 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 - 19 downloads last month - 3 stars on GitHub - 1 maintainer
biobakery-workflows 0.15.1
bioBakery workflows: A collection of meta'omic analysis workflows24 versions - Latest release: about 4 years ago - 101 downloads last month - 1 maintainer
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
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 - 5 downloads last month - 2 stars on GitHub - 1 maintainer
tasccoda 0.1.3
Tree-aggregated compositional analysis for high-throughput sequencing data4 versions - Latest release: almost 2 years ago - 1 dependent repositories - 28 downloads last month - 8 stars on GitHub - 1 maintainer
xebec 0.5.1
Snakemake pipeline for microbiome diversity effect size benchmarking.2 versions - Latest release: about 2 years ago - 1 dependent repositories - 51 downloads last month - 5 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: 2 months ago - 5 downloads last month - 1 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 - 170 downloads last month - 6 stars on GitHub - 2 maintainers
ubiome 0.6.5
uBiome core taxonomy library7 versions - Latest release: almost 8 years ago - 2 dependent repositories - 38 downloads last month - 66 stars on GitHub - 1 maintainer
woltka 0.1.6
versatile meta-omic data classifier5 versions - Latest release: 4 months ago - 1 dependent repositories - 48 downloads last month - 64 stars on GitHub - 1 maintainer
metawibele 0.4.7
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome10 versions - Latest release: 9 months ago - 1 dependent repositories - 43 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 - 34 downloads last month - 7 stars on GitHub - 2 maintainers
anadama2 0.10.0
AnADAMA2: Another Automated Data Analysis Management Application 221 versions - Latest release: almost 2 years ago - 1 dependent package - 3 dependent repositories - 129 downloads last month - 1 maintainer
panphlan 1.3
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *i...2 versions - Latest release: about 4 years ago - 1 dependent repositories - 19 downloads last month - 39 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
10 versions - Latest release: over 1 year ago - 1 dependent package - 4 dependent repositories - 282 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 - 282 downloads last month - 43 stars on GitHub - 1 maintainer
qadabra 0.3.0
Differential abundance workflow for microbiome data2 versions - Latest release: 5 months ago - 8 downloads last month - 13 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 - 20 downloads last month - 5 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 - 9 downloads last month - 0 stars on GitHub - 1 maintainer
micone 0.15.0
The Microbial Co-occurrence Network Explorer28 versions - Latest release: 9 months ago - 1 dependent repositories - 79 downloads last month - 18 stars on GitHub - 1 maintainer
q2-micom 0.14.0
QIIME 2 plugin for metabolic modeling of microbial communities.20 versions - Latest release: about 2 months ago - 1 dependent repositories - 554 downloads last month - 10 stars on GitHub - 1 maintainer
mitre 1.0b1
Microbiome Interpretable Temporal Rule Engine6 versions - Latest release: over 5 years ago - 1 dependent repositories - 45 downloads last month - 45 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 - 23 downloads last month - 1 stars on GitHub - 1 maintainer
qiita-spots 0.2.0
Qiita: Spot Patterns3 versions - Latest release: almost 9 years ago - 12 dependent repositories - 25 downloads last month - 118 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 - 14 downloads last month - 2 maintainers
kneaddata 0.12.0
13 versions - Latest release: over 1 year ago - 1 dependent repositories - 229 downloads last month - 1 maintainerhumann 3.6.1
HUMAnN: The HMP Unified Metabolic Analysis Network, version 315 versions - Latest release: over 1 year ago - 1 dependent repositories - 857 downloads last month - 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 - 91 downloads last month - 19 stars on GitHub - 2 maintainers
shortbred 0.9.5
ShortBRED: a system for profiling protein families of interest at very high specificity in shotgu...1 version - Latest release: about 4 years ago - 1 dependent repositories - 14 downloads last month - 1 maintainer
humann2 2.8.2
HUMAnN2: The HMP Unified Metabolic Analysis Network 225 versions - Latest release: about 4 years ago - 6 dependent repositories - 162 downloads last month - 1 maintainer
xlassify 1.0.0
An alignment-free deep-learning model trained to classify human gut bacteria2 versions - Latest release: over 2 years ago - 1 dependent repositories - 18 downloads last month - 1 maintainer
microbiome-toolbox 1.0.2
Microbiome Toolbox12 versions - Latest release: over 2 years ago - 1 dependent repositories - 70 downloads last month - 8 stars on GitHub - 1 maintainer
micom 0.35.0
Microbial community modeling based on cobrapy.106 versions - Latest release: about 2 months ago - 1 dependent package - 1 dependent repositories - 1.47 thousand downloads last month - 77 stars on GitHub - 1 maintainer
amptk 1.6.0
AMPtk: amplicon tool kit11 versions - Latest release: 7 months ago - 1 dependent repositories - 116 downloads last month - 35 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 - 38 downloads last month - 5 stars on GitHub - 1 maintainer
amon-bio 1.0.4
Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins f...5 versions - Latest release: 4 months ago - 51 downloads last month - 17 stars on GitHub - 2 maintainers
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
pymgpipe 0.16.10
Community level microbiome metabolic modeling in Python5 versions - Latest release: 11 months ago - 42 downloads last month - 6 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
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
Related Keywords
bioinformatics
35
python
13
microbiology
10
metagenomics
9
microbial
8
metagenomic
7
microbiome-analysis
6
qiime
6
visualization
5
metatranscriptomic
5
machine-learning
5
metabolic-models
4
qiime2
4
computational-biology
4
analysis
4
anadama2
4
cross-platform
4
humann
3
genomics
3
metabolism
3
modeling
3
pipeline
3
metagenome
2
metabolite
2
cobra
2
neural-network
2
community
2
data-analysis
2
bayesian-inference
2
hacktoberfest
2
metagenome-assembled-genomes
2
slurm
2
phylogenetics
2
dbbact
2
database
2
pbs
2
microbial-genomics
2
hpc
2
16s
2
16S
2
microbial ecology
2
heatmap
2
QIIME
2
snakemake
2
NMDC
2
reproducible-research
2
tensorflow
2
open-science
2
open-source
2
data-format
2
open-data
2
microbial-taxonomy
2
ordination
2
workflow
2
systems-biology
2
metagenomes
1
kmer
1
grid
1
anadama
1
gene-composition
1
pangenome
1
biom
1
differential-abundance
1
16s-rrna
1
sequence-bloom-trees
1
reference-genomes
1
network-analysis
1
databases
1
sequence bloom trees
1
profiling
1
metagenome-assembled genomes
1
nextflow
1
genomes
1
16s-seq
1
classification
1
characterization
1
time-series
1
statistical-analysis
1
simulation-framework
1
microbial-ecology
1
biological-simulations
1
coi
1
fungi
1
lsu
1
mtco1
1
mycobiome
1
next-generation-sequencing
1
rdna
1
virus
1
classifier
1
RNA
1
DNA
1
metabolome
1
omics-data-integration
1
exploratory
1
jupyter-notebook
1
flux-balance-analysis
1
metabolic-reconstruction
1
mgpipe
1
microbiome-modeling-toolbox
1