Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "Bioinformatics" keyword
smbl 1.4.5
SnakeMake Bioinformatics Library.24 versions - Latest release: over 8 years ago - 1 dependent repositories - 74 downloads last month - 23 stars on GitHub - 1 maintainer
treesak 1.35.1
BioSAK193 versions - Latest release: 5 days ago - 4.42 thousand downloads last month - 1 stars on GitHub - 1 maintainer
biosak 1.88.10
BioSAK413 versions - Latest release: 13 days ago - 1 dependent repositories - 3.78 thousand downloads last month - 7 stars on GitHub - 1 maintainer
Top 8.9% on pypi.org
27 versions - Latest release: almost 6 years ago - 1 dependent package - 8 dependent repositories - 101 downloads last month - 87 stars on GitHub - 1 maintainer
goenrich 1.10.2
GO enrichment with python -- pandas meets networkx27 versions - Latest release: almost 6 years ago - 1 dependent package - 8 dependent repositories - 101 downloads last month - 87 stars on GitHub - 1 maintainer
biobb-pytorch 4.1.3
biobb_pytorch is the Biobb module collection to create and train ML & DL models.4 versions - Latest release: 14 days ago - 424 downloads last month - 1 stars on GitHub - 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
biobb-radiospineomics 1.1.20
Biobb_Radiospineomics is a wrapped code for the extraction of conventional IVD features and radio...22 versions - Latest release: 2 months ago - 75 downloads last month - 0 stars on GitHub - 1 maintainer
y-lineagetracker 1.3.0
Y-LineageTracker: A framework to fully analyze human Y-chromosome sequencing data5 versions - Latest release: about 3 years ago - 1 dependent repositories - 41 downloads last month - 1 maintainer
tidepy 1.3.8
A computational method to predict immunotherapy response.11 versions - Latest release: over 1 year ago - 1 dependent repositories - 491 downloads last month - 30 stars on GitHub - 1 maintainer
mach2viz 0.0.3 removed
Online interactive visualizer for Migration Analysis of Clonal History 2 (MACH2)1 version - Latest release: 12 months ago - 8 downloads last month - 2 stars on GitHub - 1 maintainer
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
stochpy 1.1.2
StochPy (Stochastic modeling in Python) provides several stochastic simulation algorithms to simu...13 versions - Latest release: over 10 years ago - 1 dependent repositories - 204 downloads last month - 39 stars on GitHub - 2 maintainers
readtagger 0.5.25
Tags reads in a BAM file based on other BAM files.77 versions - Latest release: about 4 years ago - 1 dependent repositories - 298 downloads last month - 2 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
bioid 1.0
A python package for autonomously identifying Bioinformatic file formats.1 version - Latest release: over 8 years ago - 15 downloads last month - 0 stars on GitHub - 1 maintainer
pymantra 1.0.2
Reaction-Centred Metabolic Network Analysis4 versions - Latest release: 6 months ago - 500 downloads last month - 4 stars on GitHub - 1 maintainer
jla-demultiplexer 0.0.8
Internal lab use tool for 3 end analysis8 versions - Latest release: about 2 years ago - 1 dependent repositories - 51 downloads last month - 0 stars on GitHub - 1 maintainer
bio-mosaic 1.0
https://github.com/cyrusmaher/mosaic1 version - Latest release: over 10 years ago - 13 downloads last month - 1 stars on GitHub - 1 maintainer
molmarbles 0.1.0
A bridge between Biotite and OpenMM1 version - Latest release: over 1 year ago - 10 downloads last month - 8 stars on GitHub - 2 maintainers
gsea-incontext 0.9.6
GSEA-InContext Gene Set Enrichment Analysis in Python3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 32 downloads last month - 10 stars on GitHub - 1 maintainer
biobb-flexserv 4.1.0
biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.7 versions - Latest release: 9 months ago - 56 downloads last month - 1 stars on GitHub - 2 maintainers
drug2ways 0.0.12
Reasoning over polar paths in biological networks for drug discovery applications12 versions - Latest release: almost 2 years ago - 2 dependent repositories - 69 downloads last month - 26 stars on GitHub - 1 maintainer
biobb-gromacs 4.1.1
biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations.6 versions - Latest release: 8 months ago - 1 dependent package - 164 downloads last month - 1 stars on GitHub - 2 maintainers
biobb-common 4.2.0
Biobb_common is the base package required to use the biobb packages.27 versions - Latest release: 7 days ago - 21 dependent packages - 1 dependent repositories - 712 downloads last month - 0 stars on GitHub - 2 maintainers
biobb-model 4.1.0
Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or ...34 versions - Latest release: 8 months ago - 1 dependent package - 1 dependent repositories - 485 downloads last month - 1 stars on GitHub - 2 maintainers
biobb-pmx 4.1.0
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.15 versions - Latest release: 8 months ago - 1 dependent repositories - 161 downloads last month - 2 stars on GitHub - 2 maintainers
fastproject 1.1.4
A python module for evaulating dimensionality reduction techniques on gene expression data.11 versions - Latest release: almost 7 years ago - 1 dependent repositories - 94 downloads last month - 35 stars on GitHub - 1 maintainer
pyranges-db 0.0.7
Database add-on for PyRanges.7 versions - Latest release: over 4 years ago - 1 dependent package - 1 dependent repositories - 112 downloads last month - 0 stars on GitHub - 1 maintainer
Top 2.3% on pypi.org
40 versions - Latest release: 13 days ago - 41 dependent packages - 78 dependent repositories - 14.5 thousand downloads last month - 506 stars on GitHub - 1 maintainer
gseapy 1.1.3
Gene Set Enrichment Analysis in Python40 versions - Latest release: 13 days ago - 41 dependent packages - 78 dependent repositories - 14.5 thousand downloads last month - 506 stars on GitHub - 1 maintainer
Top 4.7% on pypi.org
23 versions - Latest release: 28 days ago - 1 dependent package - 5 dependent repositories - 10.4 thousand downloads last month - 130 stars on GitHub - 1 maintainer
geoparse 2.0.4
Python library to access Gene Expression Omnibus Database (GEO)23 versions - Latest release: 28 days ago - 1 dependent package - 5 dependent repositories - 10.4 thousand downloads last month - 130 stars on GitHub - 1 maintainer
biobb-vs 4.1.2
Biobb_vs is the Biobb module collection to perform virtual screening studies.12 versions - Latest release: 14 days ago - 1 dependent repositories - 197 downloads last month - 1 stars on GitHub - 1 maintainer
pdbviewer 0.1.2
Automatically retrieve a PDB file for a given RCSB PDB id and visualize its 3D structure.3 versions - Latest release: 23 days ago - 192 downloads last month - 0 stars on GitHub - 1 maintainer
fastqtofastaconverter 0.1
FastQ to FASTA file converter1 version - Latest release: 23 days ago - 145 downloads last month - 0 stars on GitHub - 1 maintainer
pubmedwordcloud 0.1.3
PubMedWordCloud is a Python package for generating word clouds from PubMed titles.2 versions - Latest release: 2 months ago - 22 downloads last month - 0 stars on GitHub - 1 maintainer
ogu 1.52
Organelle Genome Utilities2 versions - Latest release: 28 days ago - 68 downloads last month - 20 stars on GitHub - 1 maintainer
ncbi-counts 0.1.0
Download the NCBI-generated RNA-seq count data by specifying the Series accession number(s), and ...1 version - Latest release: 6 months ago - 10 downloads last month - 1 stars on GitHub - 1 maintainer
biobb-pdb-tools 4.1.1
Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.2 versions - Latest release: 4 months ago - 22 downloads last month - 0 stars on GitHub - 2 maintainers
bioinfolearn 0.1
Bioinformatics Learn1 version - Latest release: 7 months ago - 15 downloads last month - 1 maintainer
metachip2 2.3.8
HGT detection pipeline26 versions - Latest release: 6 months ago - 141 downloads last month - 0 stars on GitHub - 1 maintainer
syngenes 1.0.2 💰
SynGenes is a Python class for standardizing Mitochondrial or Chloroplast gene nomenclatures, thi...3 versions - Latest release: 4 months ago - 15 downloads last month - 0 stars on GitHub - 1 maintainer
clean-base 0.1.2
A simple and lighweight package tor clean softwares.4 versions - Latest release: 8 months ago - 1 dependent package - 1 dependent repositories - 39 downloads last month - 0 stars on GitHub - 1 maintainer
mach2 0.0.4
Migration Analysis of Clonal History 24 versions - Latest release: 7 months ago - 45 downloads last month - 2 stars on GitHub - 1 maintainer
fastaframes 1.1.0
A very simple fasta file parser.5 versions - Latest release: 8 months ago - 50 downloads last month - 2 stars on GitHub - 1 maintainer
triplix 0.0.5
A python package to efficiently process, store and retrieve spatial genomics multi-contact data5 versions - Latest release: 7 months ago - 59 downloads last month - 0 stars on GitHub - 1 maintainer
biobb-netprop 1.12.3
Biobb_NetProp is use case to build a prioritize PPI Network through Disc4All pre-process database...1 version - Latest release: about 1 year ago - 11 downloads last month - 0 stars on GitHub - 1 maintainer
biobb-godmd 4.1.0
Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions).6 versions - Latest release: 9 months ago - 49 downloads last month - 0 stars on GitHub - 2 maintainers
augusta 1.0.5
Python package for inference of the gene regulatory network and the boolean network using RNA-Seq...7 versions - Latest release: 4 months ago - 14 downloads last month - 2 stars on GitHub - 1 maintainer
springcraft 0.3.0
Investigate molecular dynamics with elastic network models3 versions - Latest release: over 1 year ago - 1 dependent repositories - 24 downloads last month - 5 stars on GitHub - 2 maintainers
pemt 0.0.2
A tool for extractor patent literature in drug discovery4 versions - Latest release: almost 2 years ago - 22 downloads last month - 12 stars on GitHub - 1 maintainer
ciclops 0.0.4
Pipeline for building clinical outcome prediction models on training dataset and transfer learnin...4 versions - Latest release: about 2 years ago - 27 downloads last month - 0 stars on GitHub - 1 maintainer
wormtable 0.1.7
Write-once read-many data sets using Berkeley DB.16 versions - Latest release: 8 months ago - 2 dependent repositories - 59 downloads last month - 1 maintainer
uniprotscraper 0.3
UniprotScraper is a web scraping tool that specialized for Uniprot Database.3 versions - Latest release: over 2 years ago - 1 dependent repositories - 10 downloads last month - 4 stars on GitHub - 1 maintainer
tns-piler 0.0.4
Tool for finding cumulative pileups4 versions - Latest release: over 2 years ago - 1 dependent repositories - 49 downloads last month - 0 stars on GitHub - 1 maintainer
tajimas-d 2.0.2
Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.9 versions - Latest release: 27 days ago - 1 dependent repositories - 113 downloads last month - 6 stars on GitHub - 1 maintainer
seurattoadata 0.0.6
Convert seurat obj to Adata5 versions - Latest release: about 3 years ago - 1 dependent repositories - 37 downloads last month - 1 stars on GitHub - 1 maintainer
rnftools 0.3.0
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.19 versions - Latest release: about 7 years ago - 1 dependent repositories - 76 downloads last month - 14 stars on GitHub - 1 maintainer
pyntheon 0.1
An automated tool to map mutations to Post Translational Modifitcaions (PTMs)1 version - Latest release: over 7 years ago - 1 dependent repositories - 10 downloads last month - 1 maintainer
pyhgnc 0.2.4
Importing and querying HGNC data5 versions - Latest release: over 6 years ago - 1 dependent repositories - 317 downloads last month - 5 stars on GitHub - 2 maintainers
pygna 3.3.1
Geneset Network Analysis35 versions - Latest release: over 2 years ago - 1 dependent package - 1 dependent repositories - 196 downloads last month - 32 stars on GitHub - 1 maintainer
pyctd 0.5.9
Importing and querying CTD2 versions - Latest release: almost 7 years ago - 1 dependent repositories - 18 downloads last month - 10 stars on GitHub - 1 maintainer
pybiotools4p 0.0.1rc6
Wrappers of bioinformatics tools, for analysis pipeline3 versions - Latest release: over 3 years ago - 1 dependent repositories - 33 downloads last month - 0 stars on GitHub - 1 maintainer
pmtutils 0.0.1
Portable toolkit for interacting with the PyMetaTome pipeline1 version - Latest release: almost 4 years ago - 1 dependent repositories - 14 downloads last month - 1 maintainer
pannenkoek 0.1.6
A wrapper for Qiime and LEfSe analysis. Split an OTU table by time and make certain comparisons w...8 versions - Latest release: about 9 years ago - 1 dependent repositories - 20 downloads last month - 1 maintainer
ontocontext 0.9
Beta Version11 versions - Latest release: 9 months ago - 1 dependent repositories - 36 downloads last month - 0 stars on GitHub - 1 maintainer
metachip 1.10.13
HGT detection pipeline60 versions - Latest release: about 1 year ago - 1 dependent repositories - 371 downloads last month - 49 stars on GitHub - 1 maintainer
markermag 1.1.28
linking MAGs with 16S rRNA marker genes79 versions - Latest release: about 1 year ago - 1 dependent repositories - 593 downloads last month - 1 maintainer
lrgasp-tools 1.12.0
LRGASP tools17 versions - Latest release: over 2 years ago - 1 dependent repositories - 116 downloads last month - 8 stars on GitHub - 2 maintainers
lissero 0.4.9
In silico serotyping of Listeria monocytogenes9 versions - Latest release: about 3 years ago - 1 dependent repositories - 57 downloads last month - 7 stars on GitHub - 1 maintainer
labpype 0.7.8 removed
A Framework for Creating Pipeline Software12 versions - Latest release: almost 6 years ago - 1 dependent repositories - 11 downloads last month - 20 stars on GitHub - 1 maintainer
karyopype 0.1.6
Chromosomal visualization in Python.8 versions - Latest release: almost 5 years ago - 1 dependent repositories - 81 downloads last month - 9 stars on GitHub - 1 maintainer
jla-tailer 0.1.18
Tool to find 3' tailing of non-coding RNAs25 versions - Latest release: about 2 years ago - 1 dependent repositories - 191 downloads last month - 1 stars on GitHub - 1 maintainer
genomvar 0.3.0
Sequence variant analysis in Python16 versions - Latest release: over 2 years ago - 1 dependent repositories - 21 downloads last month - 0 stars on GitHub - 1 maintainer
gecos 2.0.0
Generated color schemes for sequence alignment visualizations7 versions - Latest release: almost 2 years ago - 1 dependent repositories - 63 downloads last month - 15 stars on GitHub - 2 maintainers
embl-tools-jl 0.3.3
An extension adding Launcher shortcuts to JupyterLab for EMBL Tools21 versions - Latest release: almost 4 years ago - 1 dependent repositories - 156 downloads last month - 1 stars on GitHub - 1 maintainer
dedup_hash 0.1.1
Finds and discards exact duplicate reads in fastq files.2 versions - Latest release: over 7 years ago - 16 downloads last month - 0 stars on GitHub - 1 maintainer
congas-old 0.0.4
Copy Number genotyping from single cell RNA sequencing4 versions - Latest release: over 2 years ago - 8 downloads last month - 10 stars on GitHub - 1 maintainer
congas 0.0.78
Copy Number genotyping from single cell RNA sequencing63 versions - Latest release: 8 months ago - 441 downloads last month - 10 stars on GitHub - 1 maintainer
biobb-structure-checking 3.13.4
BioBB_structure_checking performs MDWeb structure checking tool set as a command line utility.35 versions - Latest release: 8 months ago - 3 dependent packages - 1 dependent repositories - 453 downloads last month - 8 stars on GitHub - 2 maintainers
clep 0.0.3
A Hybrid Data and Knowledge Driven Framework for Generating Patient Representations3 versions - Latest release: 2 months ago - 1 dependent repositories - 31 downloads last month - 17 stars on GitHub - 2 maintainers
biobb-flexdyn 4.1.0
biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.6 versions - Latest release: 9 months ago - 59 downloads last month - 1 stars on GitHub - 2 maintainers
biopyutils 0.2.0
A bionformatic tookits13 versions - Latest release: over 3 years ago - 141 downloads last month - 1 stars on GitHub - 1 maintainer
bioplots 0.1.6
A data visualization package for bioinformatians and computational biologist17 versions - Latest release: about 4 years ago - 130 downloads last month - 6 stars on GitHub - 1 maintainer
biobb-wf-mutations 0.0.6
Lysozyme + Mutations workflow built using BioBB Based on the official Gromacs tutorial: http://ww...6 versions - Latest release: about 5 years ago - 1 dependent repositories - 58 downloads last month - 7 stars on GitHub - 2 maintainers
biobb-structure-utils 4.1.0
biobb_structure_utils is the Biobb module collection to perform basic manipulations on 3d structu...20 versions - Latest release: 8 months ago - 1 dependent repositories - 154 downloads last month - 2 stars on GitHub - 2 maintainers
biobb-structure-manager 3.0.2
BioBB_structure_manager is a library to efficiently load and process biomolecular 3D structures.10 versions - Latest release: about 4 years ago - 1 dependent package - 1 dependent repositories - 112 downloads last month - 1 stars on GitHub - 2 maintainers
biobb-remote 1.2.2
Biobb_remote is the Biobb module for remote execution via ssl.3 versions - Latest release: over 2 years ago - 1 dependent repositories - 45 downloads last month - 1 stars on GitHub - 2 maintainers
biobb-md 3.7.2
Deprecated Package: biobb_md is no longer maintained and has been superseded by the biobb_gromacs...19 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 147 downloads last month - 7 stars on GitHub - 2 maintainers
biobb-ml 4.1.0
Biobb_ml is the Biobb module collection to perform machine learning predictions.11 versions - Latest release: 9 months ago - 1 dependent repositories - 82 downloads last month - 1 stars on GitHub - 1 maintainer
biobb-disgenet 1.1.28
Biobb_disgenet is a complete code wrapper to interrogate the DisGeNET database REST API.60 versions - Latest release: over 2 years ago - 387 downloads last month - 1 stars on GitHub - 1 maintainer
biobb-disc4alldata 0.0.12
Biobb_disc4alldata is a complete code wrapper to interrogate the Disc4All pre-process database RE...12 versions - Latest release: about 2 years ago - 127 downloads last month - 1 stars on GitHub - 1 maintainer
biobb-analysis 4.1.0
Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.39 versions - Latest release: 9 months ago - 2 dependent packages - 1 dependent repositories - 409 downloads last month - 3 stars on GitHub - 2 maintainers
biobb-cmip 4.1.1
biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.14 versions - Latest release: 3 months ago - 1 dependent repositories - 113 downloads last month - 0 stars on GitHub - 2 maintainers
biobb 1.0.2
Biobb module collection.3 versions - Latest release: about 5 years ago - 1 dependent repositories - 43 downloads last month - 48 stars on GitHub - 2 maintainers
bedqr 0.4.6
2 versions - Latest release: almost 2 years ago - 340 downloads last month - 1 maintainerbatchadapt 1.2
Dynamic multi-loci/multi-repeat tract microsatellite reference sequence generator7 versions - Latest release: about 4 years ago - 2 dependent repositories - 80 downloads last month - 0 stars on GitHub - 1 maintainer
ammolite 0.8.0
Visualize structure data from Biotite with PyMOL9 versions - Latest release: almost 2 years ago - 2 dependent repositories - 89 downloads last month - 16 stars on GitHub - 2 maintainers
ctrlf-tf 1.0b4
Protein-DNA binding site caller from kmer data5 versions - Latest release: 11 months ago - 76 downloads last month - 2 stars on GitHub - 1 maintainer
syba 0.0.5
SyBA: a tool and database for standardizing gene names from the main bacterial pathogens causing ...2 versions - Latest release: 2 months ago - 38 downloads last month - 1 stars on GitHub - 1 maintainer
biobb-io 4.1.1
Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb bui...28 versions - Latest release: 14 days ago - 1 dependent package - 1 dependent repositories - 451 downloads last month - 2 stars on GitHub - 2 maintainers
biobb-chemistry 4.1.0
Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simul...21 versions - Latest release: 9 months ago - 1 dependent repositories - 186 downloads last month - 4 stars on GitHub - 2 maintainers
Related Keywords
Compatibility
32
BioExcel
32
Workflows
32
bioinformatics
18
Computational Biology
7
Metagenomics
6
Genomics
5
Computational biology
5
Biology
5
Cancer
4
metagenomics
4
Protein
4
Enrichment
4
Gene Ontology
4
GO
4
Phylogeny
3
Python
3
FASTA
3
genomics
3
Computational Biologist
3
Sequencing
3
python
3
Flexibility
2
Ensembles
2
ncRNAs
2
Structure
2
pipeline
2
Data-analysis
2
Genetic-references
2
systems-biology
2
Drug Discovery
2
XML
2
drug-discovery
2
NCBI
2
Genes
2
Synonymous
2
scRNA
2
scDNA
2
Data visualization
2
RNA
2
CNV
2
CNA
2
Copy-number
2
Gene Expression Omnibus
2
HGT_detection
2
GEO
2
enrichment-analysis
2
rna-seq
2
proteomics
2
Genome
2
Ontology
2
Computational Systems Biology
2
lgt
2
Refinement
2
Binning
2
lateral-gene-transfer
2
pandas
2
Modeling
2
Simulation
2
horizontal-gene-transfer
2
Machine Learning
2
hgt
2
simulator
2
visualization
2
Transcriptomics
2
Metastasis
2
biology
2
Genetics
2
Computational
2
read-simulation
1
GUI
1
Widget
1
Workflow
1
Pipeline
1
serotyping
1
public-health
1
microbial-genomics
1
listeria-monocytogenes
1
Protein variants
1
PTMs
1
ngs-format
1
ngs
1
mapper-evaluation
1
framework
1
visualprogramming
1
widget
1
watterson-estimator
1
workflow
1
tamija
1
population-genetics
1
Sequence
1
network-biology
1
biostatistics
1
networkx
1
Statistics
1
pygna
1
Toxicogenomics
1
Database
1
Human health
1
Wrappers
1