Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "metagenomics" keyword
resmico 1.2.2
Increasing the quality of metagenome-assembled genomes with deep learning18 versions - Latest release: over 1 year ago - 1 dependent repositories - 27 downloads last month - 9 stars on GitHub - 1 maintainer
cmash 0.3.0
Fast and accurate set similarity estimation via containment min hash (for genomic datasets).7 versions - Latest release: over 6 years ago - 1 dependent repositories - 55 downloads last month - 42 stars on GitHub - 1 maintainer
mglex 0.2.1
MGLEX - MetaGenome Likelihood EXtractor3 versions - Latest release: about 6 years ago - 1 dependent repositories - 14 downloads last month - 6 stars on GitHub - 1 maintainer
Top 9.6% on pypi.org
1 version - Latest release: 10 months ago - 2 dependent repositories - 1 maintainer
metacram 0.5
Comparative Rapid Annotation of Metagenomes1 version - Latest release: 10 months ago - 2 dependent repositories - 1 maintainer
strainflair 0.0.2
StrainFLAIR (STRAIN-level proFiLing using vArIation gRaph) is a tool for strain identification an...1 version - Latest release: over 3 years ago - 1 dependent repositories - 13 downloads last month - 24 stars on GitHub - 1 maintainer
randmag 1.2.0
Construct artifical MAGs from complete genomes according to distribution3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 6 downloads last month - 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
prophyle 0.1.0
ProPhyle metagenomic classifier54 versions - Latest release: about 7 years ago - 1 dependent repositories - 240 downloads last month - 31 stars on GitHub - 1 maintainer
mvirs 1.1.1
mVIRs: Localisation of inducible prophages using NGS data1 version - Latest release: about 2 years ago - 1 dependent repositories - 10 downloads last month - 12 stars on GitHub - 1 maintainer
crocodeel 1.0.3
CroCoDeEL is a tool that detects cross-sample (aka well-to-well) contamination in shotgun metagen...5 versions - Latest release: 27 days ago - 487 downloads last month - 4 stars on GitHub - 1 maintainer
nglesspy 0.2.2
NGLessPy: Python interface to NGLess3 versions - Latest release: almost 6 years ago - 1 dependent repositories - 12 downloads last month - 2 stars on GitHub - 1 maintainer
pynteny 0.0.2 removed
Multiple HMM - search via synteny structures in Python1 version - Latest release: over 1 year ago - 20 downloads last month - 5 stars on GitHub
taxpasta 0.6.1
TAXonomic Profile Aggregation and STAndardisation12 versions - Latest release: 8 months ago - 76 downloads last month - 27 stars on GitHub - 3 maintainers
arg-ranker 3.7.2
Ranking the risk of antibiotic resistance for genomes/metagenomes31 versions - Latest release: 5 months ago - 169 downloads last month - 22 stars on GitHub - 1 maintainer
kraken-biom 1.0.1
Create BIOM-format tables from Kraken output.1 version - Latest release: almost 8 years ago - 1 dependent repositories - 134 downloads last month - 44 stars on GitHub - 1 maintainer
metapathways_python v2.1
A pipeline for MetaGenomic analysis which is capable of creating ePGDBs using Pathway Tools2 versions - Latest release: almost 10 years ago - 8 downloads last month - 1 maintainer
mtags 1.0.4
mTAGs - taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene.2 versions - Latest release: over 2 years ago - 1 dependent repositories - 8 downloads last month - 6 stars on GitHub - 1 maintainer
cobra-meta 1.2.3
COBRA (Contig Overlap Based Re-Assembly) is a bioinformatics tool to get higher quality viral gen...4 versions - Latest release: 3 months ago - 37 downloads last month - 43 stars on GitHub - 1 maintainer
mdeepfri 1.1.5
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.5 versions - Latest release: 2 months ago - 56 downloads last month - 29 stars on GitHub - 1 maintainer
metagenome-atlas 2.0.0
ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscript...2 versions - Latest release: over 5 years ago - 1 dependent repositories - 26 downloads last month - 346 stars on GitHub - 2 maintainers
toolchest-client 0.11.14
Python client for Toolchest84 versions - Latest release: about 1 year ago - 1 dependent package - 2 dependent repositories - 620 downloads last month - 15 stars on GitHub - 2 maintainers
virstrain 1.17
An RNA/DNA virus strain-level identification tool for short reads.7 versions - Latest release: 3 months ago - 1 dependent repositories - 131 downloads last month - 19 stars on GitHub - 1 maintainer
clark-biom 1.0.0
Create BIOM-format tables from CLARK abundance tables.1 version - Latest release: about 6 years ago - 1 dependent repositories - 30 downloads last month - 1 stars on GitHub - 1 maintainer
ancientmetagenomedircheck 1.2.1
Performs validity check of ancientMetagenomeDir datasets6 versions - Latest release: over 3 years ago - 57 downloads last month - 2 stars on GitHub - 1 maintainer
woltka 0.1.6
versatile meta-omic data classifier5 versions - Latest release: 3 months ago - 1 dependent repositories - 48 downloads last month - 64 stars on GitHub - 1 maintainer
magpurify 2.1.2
Identify and remove incorrectly binned contigs from metagenome-assembled genomes.5 versions - Latest release: about 4 years ago - 1 dependent repositories - 37 downloads last month - 45 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 - 19 downloads last month - 39 stars on GitHub - 1 maintainer
metator 1.3.2
A pipeline for binning metagenomic datasets from metaHiC data.31 versions - Latest release: 6 months ago - 1 dependent repositories - 102 downloads last month - 20 stars on GitHub - 4 maintainers
pathogentrack 0.2.3
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data1 version - Latest release: over 2 years ago - 1 dependent repositories - 10 downloads last month - 24 stars on GitHub - 1 maintainer
ymp 0.2.1
Flexible multi-omic pipeline system6 versions - Latest release: almost 4 years ago - 1 dependent repositories - 38 downloads last month - 18 stars on GitHub - 1 maintainer
qadabra 0.3.0
Differential abundance workflow for microbiome data2 versions - Latest release: 4 months ago - 8 downloads last month - 13 stars on GitHub - 1 maintainer
taxamatcher 1.0.1
Easy to use taxonomy correlator1 version - Latest release: about 5 years ago - 1 dependent repositories - 17 downloads last month - 0 stars on GitHub - 1 maintainer
macrel 1.3.0
MACREL6 versions - Latest release: 6 months ago - 1 dependent repositories - 20 downloads last month - 50 stars on GitHub - 1 maintainer
impy 0.2.8
Integrated Metaomic Pipeline command-line utility.13 versions - Latest release: about 7 years ago - 1 dependent repositories - 45 downloads last month - 1 maintainer
metachip 1.10.13
HGT detection pipeline60 versions - Latest release: about 1 year ago - 1 dependent repositories - 321 downloads last month - 51 stars on GitHub - 1 maintainer
micomplete 1.1.1
Quality control of assembled genomes9 versions - Latest release: almost 5 years ago - 1 dependent package - 1 dependent repositories - 41 downloads last month - 2 maintainers
genomeuploader 2.0.0 removed
Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This ...1 version - Latest release: about 1 month ago - 1 maintainer
fetch-tool 0.9.0
Utility to fetch public and private RAW read and assembly files from the ENA5 versions - Latest release: 9 months ago - 32 downloads last month - 2 stars on GitHub - 2 maintainers
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
Top 7.4% on pypi.org
48 versions - Latest release: about 1 month ago - 2 dependent repositories - 592 downloads last month - 430 stars on GitHub - 3 maintainers
gtdbtk 2.4.0
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.48 versions - Latest release: about 1 month ago - 2 dependent repositories - 592 downloads last month - 430 stars on GitHub - 3 maintainers
mgnify-pipelines-toolkit 0.1.2
Collection of scripts and tools for MGnify pipelines9 versions - Latest release: about 1 month ago - 43 downloads last month - 1,561 stars on GitHub - 1 maintainer
metav 1.0
rapid detection and classification of viruses in metagenomics sequencing.3 versions - Latest release: 17 days ago - 230 downloads last month - 3 stars on GitHub - 1 maintainer
metacoag 1.2.0
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs6 versions - Latest release: about 1 month ago - 112 downloads last month - 42 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
39 versions - Latest release: 3 months ago - 4 dependent repositories - 305 downloads last month - 172 stars on GitHub - 1 maintainer
insilicoseq 2.0.1
a sequencing simulator39 versions - Latest release: 3 months ago - 4 dependent repositories - 305 downloads last month - 172 stars on GitHub - 1 maintainer
senseppi 0.7.1
SENSE-PPI: Sequence-based EvolutioNary ScalE Protein-Protein Interaction prediction17 versions - Latest release: about 2 months ago - 81 downloads last month - 1,273 stars on GitHub - 1 maintainer
gdmicro 1.0.10
GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut ...10 versions - Latest release: 7 months ago - 61 downloads last month - 7 stars on GitHub - 1 maintainer
graphbin 1.7.1
graphbin: Refined binning of metagenomic contigs using assembly graphs.4 versions - Latest release: 10 months ago - 1 dependent repositories - 63 downloads last month - 81 stars on GitHub - 1 maintainer
meta-sparse 0.1.12
SPARSE indexes reference genomes in public databases into hierarchical clusters and uses it to pr...12 versions - Latest release: over 5 years ago - 1 dependent repositories - 30 downloads last month - 17 stars on GitHub - 1 maintainer
metaphlan 4.1.0
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteri...26 versions - Latest release: 3 months ago - 1 dependent repositories - 1.42 thousand downloads last month - 273 stars on GitHub - 2 maintainers
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
muttui 2.0.2
A pipeline to reconstruct mutational spectra for bacterial and viral datasets3 versions - Latest release: almost 2 years ago - 28 downloads last month - 25 stars on GitHub - 1 maintainer
sixgill 0.2.4
six-frame genome-inferred libraries for LC-MS/MS8 versions - Latest release: over 7 years ago - 2 dependent repositories - 55 downloads last month - 1 maintainer
sgtree 0.0.10
Computational pipeline for fast and easy construction of phylogenetic trees.1 version - Latest release: almost 4 years ago - 1 dependent repositories - 5 downloads last month - 1 maintainer
binning-refiner 1.4.3
Binning_refiner4 versions - Latest release: over 3 years ago - 1 dependent repositories - 48 downloads last month - 30 stars on GitHub - 1 maintainer
pyyamb 0.1.4
Yet Another Metagenome Binner8 versions - Latest release: 8 months ago - 48 downloads last month - 0 stars on GitHub - 1 maintainer
pnnl-atlas 1.0.32
ATLAS - a framework for assembly, annotation, and genomic binning of metagenomic and metatranscri...12 versions - Latest release: about 6 years ago - 1 dependent repositories - 71 downloads last month - 320 stars on GitHub - 1 maintainer
amdirt 1.6.0
AMDirT: AncientMetagenomeDir Toolkit9 versions - Latest release: about 2 months ago - 1 dependent repositories - 94 downloads last month - 2 stars on GitHub - 1 maintainer
anvio 2.4.0
An interactive analysis and visualization platform for 'omics data. See https://merenlab.org/proj...29 versions - Latest release: almost 7 years ago - 2 dependent repositories - 95 downloads last month - 1 maintainer
metapathways 3.1.6
MetaPathways is a modular pipeline to build PGDBs from Metagenomic sequences.1 version - Latest release: over 3 years ago - 1 dependent repositories - 8 downloads last month - 0 stars on GitHub - 2 maintainers
hgtsim 1.1.0
a simulator for HGT in microbial communities1 version - Latest release: over 5 years ago - 1 dependent repositories - 11 downloads last month - 8 stars on GitHub - 1 maintainer
binette 1.0.0
Binette: accurate binning refinement tool to constructs high quality MAGs.3 versions - Latest release: 4 months ago - 25 downloads last month - 5 stars on GitHub - 1 maintainer
zol 1.2.1
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e....2 versions - Latest release: about 1 year ago - 27 downloads last month - 34 stars on GitHub - 1 maintainer
gmgc-mapper 0.2.0
Map genes and genome to the Global Microbial Gene Catalog (GMGC)2 versions - Latest release: almost 4 years ago - 1 dependent repositories - 11 downloads last month - 6 stars on GitHub - 1 maintainer
hundo 1.2.8
Amplicon processing protocol31 versions - Latest release: almost 5 years ago - 1 dependent repositories - 202 downloads last month - 14 stars on GitHub - 1 maintainer
metaron 3.0
Metagenomic opeRon prediction pipeline4 versions - Latest release: about 2 years ago - 1 dependent repositories - 43 downloads last month - 6 stars on GitHub - 1 maintainer
spacegraphcats 2.1.2
tools for biological assembly graph neighborhood analysis15 versions - Latest release: over 1 year ago - 1 dependent repositories - 65 downloads last month - 117 stars on GitHub - 1 maintainer
magpurify2 1.0.2
Identify and remove contaminants from metagenome-assembled genomes.3 versions - Latest release: about 1 year ago - 61 downloads last month - 14 stars on GitHub - 1 maintainer
cocopye 0.4.0
Feature-based prediction of genome quality indices11 versions - Latest release: 4 months ago - 93 downloads last month - 1 stars on GitHub - 1 maintainer
phageboost 0.1.7
a Fast Prophage and Phage Predictor5 versions - Latest release: over 3 years ago - 1 dependent repositories - 56 downloads last month - 32 stars on GitHub - 1 maintainer
aviary-genome 0.9.1
aviary - metagenomics pipeline using long and short reads21 versions - Latest release: 19 days ago - 193 downloads last month - 68 stars on GitHub - 3 maintainers
combined-gene-caller 1.0.4
Combined gene caller for MGnify pipeline, to combine predictions from FragGeneScan and Prodigal2 versions - Latest release: 10 months ago - 25 downloads last month - 0 stars on GitHub - 2 maintainers
motulizer 0.3.2
making OTUs from genomes, and stats on them. and even core-genomes16 versions - Latest release: over 2 years ago - 1 dependent repositories - 197 downloads last month - 11 stars on GitHub - 1 maintainer
pydamage 0.72
Damage parameter estimation for ancient DNA14 versions - Latest release: 9 months ago - 1 dependent repositories - 90 downloads last month - 8 stars on GitHub - 1 maintainer
genome-uploader 2.1.0
Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This ...3 versions - Latest release: about 1 month ago - 316 downloads last month - 20 stars on GitHub - 1 maintainer
graphbin2 1.2.3
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs2 versions - Latest release: about 1 month ago - 451 downloads last month - 27 stars on GitHub - 1 maintainer
assnake 0.8.9
System for metagenomics data analysis8 versions - Latest release: about 4 years ago - 1 dependent repositories - 51 downloads last month - 11 stars on GitHub - 1 maintainer
convertfq 0.1.0
convertFQ is used to convert either DNA2RNA or RNA2DNA in a fastq file1 version - Latest release: almost 2 years ago - 13 downloads last month - 0 stars on GitHub - 1 maintainer
meteor 2.0.10
Meteor - A plateform for quantitative metagenomic profiling of complex ecosystems11 versions - Latest release: 24 days ago - 1 dependent repositories - 604 downloads last month - 6 stars on GitHub - 1 maintainer
strainscan 1.0.14
One efficient and accurate strain-level microbiome composition analysis tool based on reference g...14 versions - Latest release: 8 months ago - 1 dependent repositories - 79 downloads last month - 30 stars on GitHub - 1 maintainer
tiara 1.0.3
A tool for classifying metagenomic data4 versions - Latest release: over 1 year ago - 1 dependent repositories - 111 downloads last month - 44 stars on GitHub - 1 maintainer
superpang 1.3.0
Non-redundant pangenome assemblies from multiple genomes or bins18 versions - Latest release: 3 months ago - 1 dependent repositories - 25 downloads last month - 11 stars on GitHub - 1 maintainer
singlem 0.17.0
Novelty-inclusive microbial community profiling of shotgun metagenomes17 versions - Latest release: 22 days ago - 1 dependent repositories - 134 downloads last month - 103 stars on GitHub - 2 maintainers
s3n2bin 0.1.1
Metagenomic binning with semi-supervised siamese neural network2 versions - Latest release: about 3 years ago - 1 dependent repositories - 16 downloads last month - 98 stars on GitHub - 1 maintainer
phenotrex 0.6.0
Microbial Phenotype Prediction4 versions - Latest release: over 2 years ago - 1 dependent repositories - 54 downloads last month - 8 stars on GitHub - 2 maintainers
microwinebar 0.0.1
MicroWineBar1 version - Latest release: almost 5 years ago - 1 dependent repositories - 14 downloads last month - 4 stars on GitHub - 1 maintainer
mgkit 0.5.8
Metagenomics Framework30 versions - Latest release: over 2 years ago - 2 dependent repositories - 147 downloads last month - 12 stars on GitHub - 1 maintainer
living-tree 0.0.6
An efficient toolkit for constructing and processing taxonomic trees (metagenomic reads count, re...5 versions - Latest release: over 2 years ago - 2 dependent repositories - 48 downloads last month - 4 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 - 81 downloads last month - 1 stars on GitHub - 2 maintainers
gecco-tool 0.9.10
Gene cluster prediction with Conditional random fields.29 versions - Latest release: 3 months ago - 1 dependent repositories - 283 downloads last month - 52 stars on GitHub - 2 maintainers
famli 1.2
Functional Analysis of Metagenomes by Likelihood Inferrence3 versions - Latest release: over 4 years ago - 1 dependent repositories - 33 downloads last month - 16 stars on GitHub - 1 maintainer
enrichm 0.6.5
enrichm is a toolbox for comparing the functional composition of population genomes42 versions - Latest release: over 1 year ago - 1 dependent repositories - 161 downloads last month - 78 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
deepmased 0.3.1
Deep learning for Metagenome Assembly Error Detection2 versions - Latest release: about 4 years ago - 1 dependent repositories - 24 downloads last month - 25 stars on GitHub - 1 maintainer
coconet-binning 1.1.0
A contig binning tool from viral metagenomes11 versions - Latest release: about 3 years ago - 1 dependent repositories - 53 downloads last month - 13 stars on GitHub - 1 maintainer
chfilter 1.3
Simple instructions to remove 16s rRNA reads from metagenomics samples2 versions - Latest release: over 6 years ago - 1 dependent repositories - 16 downloads last month - 0 stars on GitHub - 1 maintainer
jaeger-bio 1.1.251
A quick and precise pipeline for detecting phages in sequence assemblies.4 versions - Latest release: about 2 months ago - 377 downloads last month - 18 stars on GitHub - 1 maintainer
phables 1.3.2
Phables: from fragmented assemblies to high-quality bacteriophage genomes21 versions - Latest release: 2 months ago - 1 dependent repositories - 72 downloads last month - 62 stars on GitHub - 1 maintainer
midas2 1.1.3
https://midas2.readthedocs.io/en/latest/16 versions - Latest release: 6 months ago - 1 dependent repositories - 116 downloads last month - 31 stars on GitHub - 1 maintainer
recentrifuge 1.14.0
Robust comparative analysis and contamination removal for metagenomics82 versions - Latest release: 4 months ago - 1 dependent repositories - 477 downloads last month - 83 stars on GitHub - 1 maintainer
motu-profiler 3.1.0
Taxonomic profiling of metagenomes from diverse environments with mOTUs33 versions - Latest release: about 1 year ago - 3 dependent repositories - 37 downloads last month - 141 stars on GitHub - 1 maintainer
Related Keywords
bioinformatics
65
genomics
18
python
11
microbiome
9
binning
7
microbiology
7
deep-learning
6
ngs
6
taxonomic-classification
6
taxonomy
6
Metagenomics
6
pipeline
5
snakemake
5
assembly
5
pangenome
4
Bioinformatics
4
biology
4
machine-learning
4
classification
4
workflow
4
bacteria
4
NGS
3
sequencing
3
computational-biology
3
comparative-genomics
3
profiling
3
taxonomic-classifications
3
tool
3
clustering
3
metagenome-assembly
3
annotation
3
functional-annotation
3
ancient-dna
3
metagenome-assembled genomes
3
conda
3
metagenomic-pipeline
3
k-mers
3
metagenomic-classification
3
alignment
3
contigs
3
assembly-graphs
3
biom-format
2
hgt
2
genome
2
16s
2
metatranscriptomics
2
viruses
2
viral-metagenomics
2
deep
2
microbial-genomics
2
mmseqs
2
simulation
2
genomic-binning
2
rna-seq
2
hacktoberfest
2
virus
2
self-supervised-learning
2
clark
2
ancient-metagenomics
2
data
2
palaeogenomics
2
assembly-binning
2
strains
2
Refinement
2
Binning
2
ngless
2
phylogenetics
2
biosynthetic-gene-clusters
2
visualization
2
metagenome-assembled-genomes
2
taxonomic
2
phage
2
lgt
2
BIOM
2
kraken
2
horizontal-gene-transfer
2
lateral-gene-transfer
2
DATA
1
analysis
1
HGT
1
illumina
1
metagenomics-data
1
genome quality
1
SNP
1
metagenomic-operons
1
binning-refiner
1
bgc
1
metagenomics-binning
1
MBL
1
bioinformatics-tool
1
Prokaryote
1
converter
1
metaproteomics
1
dna-sequences
1
simulator
1
fastq
1
SNV
1
transmission
1
machine learning
1
prophage
1