Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
conda-forge.org "bioinformatics" keyword
plantcv 3.14.1
Plant phenotyping with image analysis12 versions - Latest release: over 1 year ago - 557 stars on GitHub
qubekit 2.1.1
QUBEKit is a Python based force field parameter derivation toolkit. Our aims are to allow users t...3 versions - Latest release: about 2 years ago - 76 stars on GitHub
mmcif_pdbx 2.0.0
Yet another version of PDBx/mmCIF Python implementation3 versions - Latest release: about 3 years ago - 1 dependent package - 2 dependent repositories - 5 stars on GitHub
redbiom 0.3.5
redbiom is a cache service for sample metadata and sample data. If used, please cite "redbiom: a...2 versions - Latest release: over 4 years ago - 39 stars on GitHub
peppy 0.35.3
Project metadata manager for PEPs in Python12 versions - Latest release: over 1 year ago - 1 dependent package - 23 dependent repositories - 32 stars on GitHub
biopandas 0.4.1 💰
BioPandas is a library for working with Protein Databank Files(PDB) written in Python 2.7 and Pyt...11 versions - Latest release: almost 2 years ago - 3 dependent packages - 17 dependent repositories - 621 stars on GitHub
scikit-bio 0.5.7
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data struct...7 versions - Latest release: about 2 years ago - 7 dependent packages - 32 dependent repositories - 828 stars on GitHub
tskit 0.5.3
Toolkit for storing and processing large-scale genetic genealogies.19 versions - Latest release: over 1 year ago - 4 dependent packages - 8 dependent repositories - 114 stars on GitHub
Top 8.4% on conda-forge.org
5 versions - Latest release: about 2 years ago - 6 dependent packages - 33 dependent repositories - 1,728 stars on GitHub
scanpy 1.9.1
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with an...5 versions - Latest release: about 2 years ago - 6 dependent packages - 33 dependent repositories - 1,728 stars on GitHub
apbs 1.5
APBS - software for biomolecular electrostatics and solvation1 version - Latest release: almost 5 years ago - 2 dependent packages - 1 dependent repositories - 123 stars on GitHub
pdb2pqr 3.4.1
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biom...7 versions - Latest release: over 2 years ago - 1 dependent package - 3 dependent repositories - 61 stars on GitHub
plip 2.2.2
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interacti...10 versions - Latest release: almost 3 years ago - 1 dependent package - 1 dependent repositories - 283 stars on GitHub
Top 2.5% on conda-forge.org
87 versions - Latest release: over 1 year ago - 37 dependent packages - 108 dependent repositories - 18,331 stars on GitHub
dash 2.7.0 💰
Data Apps & Dashboards for Python. No JavaScript Required.87 versions - Latest release: over 1 year ago - 37 dependent packages - 108 dependent repositories - 18,331 stars on GitHub
galaxy-tool-util 22.1.5
Data intensive science for everyone.6 versions - Latest release: over 1 year ago - 1,077 stars on GitHub
galaxy-util 22.1.1
Data intensive science for everyone.2 versions - Latest release: over 1 year ago - 2 dependent packages - 1,077 stars on GitHub
minifasta 3.0.2
A simple FASTA toolbox for small to medium size projects without dependencies.3 versions - Latest release: over 1 year ago - 3 stars on GitHub
oliver 1.4.11
An opinionated Cromwell orchestration manager.18 versions - Latest release: over 1 year ago - 36 stars on GitHub
pegasus-wms 5.0.3
Pegasus Workflow Management System Python API ============================================= This...4 versions - Latest release: over 1 year ago - 1 dependent package - 150 stars on GitHub
pegasus-wms.api 5.0.3
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.4 versions - Latest release: over 1 year ago - 2 dependent packages - 150 stars on GitHub
pegasus-wms.dax 5.0.3
The `Pegasus.DAX3` API has been deprecated and will be removed in v5.1.0. Please use the new API ...4 versions - Latest release: over 1 year ago - 1 dependent package - 150 stars on GitHub
pegasus-wms.worker 5.0.3
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.4 versions - Latest release: over 1 year ago - 1 dependent package - 150 stars on GitHub
pegasus-wms.common 5.0.3
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.4 versions - Latest release: over 1 year ago - 2 dependent packages - 150 stars on GitHub
python-pegasus-wms 5.0.1
This package contains the Python APIs for Pegasus WMS, including: - The DAX API (Versions 2 and ...6 versions - Latest release: over 2 years ago - 2 dependent packages - 4 dependent repositories - 150 stars on GitHub
doepipeline 1.1.1
A python package for optimizing processing pipelines using statistical design of experiments (DoE).2 versions - Latest release: almost 5 years ago - 20 stars on GitHub
histolab 0.5.1 💰
Library for Digital Pathology Image Processing1 version - Latest release: about 2 years ago - 229 stars on GitHub
deeppurpose 0.0.5
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinforma...2 versions - Latest release: over 3 years ago - 709 stars on GitHub
pytdc 0.3.8
Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science25 versions - Latest release: over 1 year ago - 1 dependent repositories - 771 stars on GitHub
python-codon-tables 0.1.12
Provides codon usage tables as dictionnaries, for Python 3+. Tables for the following organisms ...2 versions - Latest release: almost 2 years ago - 1 dependent package - 28 stars on GitHub
r-immunarch 0.8.0
🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-...5 versions - Latest release: over 1 year ago - 1 dependent repositories - 252 stars on GitHub
r-omicnavigator 1.11.5
Open-Source Software for Omic Data Analysis and Visualization2 versions - Latest release: almost 2 years ago - 18 stars on GitHub
cromwell 83
Scientific workflow engine designed for simplicity & scalability. Trivially transition between on...41 versions - Latest release: almost 2 years ago - 5 dependent repositories - 878 stars on GitHub
metanetx-sdk 0.5.0
The main purpose of metanetx-sdk is to download and parse the data tables provided by the [MetaNe...3 versions - Latest release: about 4 years ago - 1 dependent package - 4 stars on GitHub
crystals 1.6.0 💰
crystals provides data structure to manipulate crystal structures, including parsing crystal file...22 versions - Latest release: almost 2 years ago - 2 dependent packages - 33 stars on GitHub
orange3-bioinformatics 4.5.0 💰
Orange Bioinformatics provides access to publicly available data, like GEO data sets, GO and KEGG...20 versions - Latest release: over 2 years ago - 1 dependent package - 16 stars on GitHub
metanetx-assets 0.2.1
The tabular information coming from [MetaNetX](https://metanetx.org) requires particular transfor...6 versions - Latest release: about 4 years ago - 1 dependent package - 1 stars on GitHub
sourmash-minimal 4.5.0
This is a minimal version that avoids heavy dependencies and is as cross-platform as possible. Fo...20 versions - Latest release: over 1 year ago - 1 dependent repositories - 352 stars on GitHub
Top 3.4% on conda-forge.org
10 versions - Latest release: over 1 year ago - 24 dependent packages - 507 dependent repositories - 3,492 stars on GitHub
biopython 1.71
Biopython is a collection of freely available Python tools for computational molecular biology10 versions - Latest release: over 1 year ago - 24 dependent packages - 507 dependent repositories - 3,492 stars on GitHub
r-flowr 0.9.11
Robust and efficient workflows using a simple language agnostic approach2 versions - Latest release: about 3 years ago - 78 stars on GitHub
biotite 0.35.0
A comprehensive library for computational molecular biology28 versions - Latest release: over 1 year ago - 7 dependent packages - 5 dependent repositories - 365 stars on GitHub
r-peptides 2.4.4
An R package to calculate indices and theoretical physicochemical properties of peptides and prot...1 version - Latest release: almost 3 years ago - 1 dependent package - 65 stars on GitHub
galaxy-containers 22.1.1
Data intensive science for everyone.3 versions - Latest release: over 1 year ago - 1 dependent package - 1,077 stars on GitHub
pycashier 22.10.1
cash in on DNA barcode tags13 versions - Latest release: over 1 year ago - 3 stars on GitHub
dash-bio 1.0.2 💰
Open-source bioinformatics components for Dash5 versions - Latest release: about 2 years ago - 1 dependent package - 2 dependent repositories - 462 stars on GitHub
r-clustassess 0.3.0
Tools for assessing clustering robustness1 version - Latest release: about 2 years ago - 17 stars on GitHub
cdk 2.5
Molecule and reaction valence bond representation. Read and write file formats: SMILES, SDF, InCh...1 version - Latest release: over 2 years ago - 397 stars on GitHub
conda-env-builder 0.0.2
Build and maintain multiple custom conda environments all in one place.1 version - Latest release: over 1 year ago - 32 stars on GitHub
anndata 0.8.0
AnnData provides a scalable way of keeping track of data and learned annotations. It was initiall...10 versions - Latest release: about 2 years ago - 10 dependent packages - 17 dependent repositories - 358 stars on GitHub
allensdk 0.14.4
The Allen Software Development Kit houses source code for reading and processing Allen Brain Atla...1 version - Latest release: about 4 years ago - 290 stars on GitHub
ammolite 0.8.0
Visualize structure data from Biotite with PyMOL5 versions - Latest release: almost 2 years ago - 2 dependent repositories - 12 stars on GitHub
cobra 0.26.0
Constraint-based reconstruction and analysis (COBRA) methods are widely used for genome-scale mod...7 versions - Latest release: over 1 year ago - 3 dependent packages - 2 dependent repositories - 392 stars on GitHub
unifunc 1.4.5
UniFunc is a text mining tool that processes and analysis text similarity between a pair of prote...7 versions - Latest release: about 2 years ago - 4 stars on GitHub
tiara 1.0.3
Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data p...1 version - Latest release: over 1 year ago - 30 stars on GitHub
weblogo 3.7.12
WebLogo (https://github.com/WebLogo/weblogo) is a tool for creating sequence logos from biologica...5 versions - Latest release: almost 2 years ago - 1 dependent package - 6 dependent repositories - 120 stars on GitHub
edlib 1.3.9
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) ...1 version - Latest release: over 2 years ago - 1 dependent package - 415 stars on GitHub
dgllife 0.3.0
Python package for graph neural networks in chemistry and biology3 versions - Latest release: almost 2 years ago - 7 dependent repositories - 551 stars on GitHub
geoparse 2.0.3
Python library to access Gene Expression Omnibus Database (GEO)1 version - Latest release: over 2 years ago - 2 dependent packages - 1 dependent repositories - 118 stars on GitHub
murphy 0.1
Generic tools to support parsing gtf/gff files and identifying overlapping genomic regions1 version - Latest release: over 1 year ago - 0 stars on GitHub
dash_cytoscape 0.2.0 💰
Interactive network visualization in Python and Dash, powered by Cytoscape.js2 versions - Latest release: almost 4 years ago - 3 dependent repositories - 495 stars on GitHub
grakel 0.1.8
GraKeL is a library that provides implementations of several well-established graph kernels. The ...1 version - Latest release: over 3 years ago - 1 dependent repositories - 496 stars on GitHub
contact_map 0.7.0
Contact maps based on MDTraj; useful for studying for intramolecular and intermolecular contacts ...10 versions - Latest release: over 3 years ago - 29 stars on GitHub
qurro 0.8.0
Qurro generates interactive visualizations of feature rankings (defined as some sortable measure ...4 versions - Latest release: over 1 year ago - 23 stars on GitHub
r-homologene 1.4.68.19.3.27
:mouse: :left_right_arrow: :couple: An r package that works as a wrapper to homologene1 version - Latest release: over 2 years ago - 30 stars on GitHub
Related Keywords
workflow
12
python
9
genomics
9
hpc
8
computational-biology
7
workflow-management-system
6
hacktoberfest
6
distributed-systems
6
pipeline
6
science
5
chemistry
5
machine-learning
5
data-science
5
ngs
5
sequencing
4
dna
4
drug-discovery
4
usegalaxy
3
dash
3
cheminformatics
3
deep-learning
3
protein-structure
3
biophysics
3
workflow-engine
3
single-cell
2
biology
2
docker
2
metanetx
2
workflow-execution
2
biopython
2
sequence-alignment
2
wdl
2
cran
2
modeling
2
plotly
2
plotly-dash
2
r
2
structural-biology
2
scala
2
microbiome
2
qiime
2
biochemistry
2
protein-protein-interaction
2
cloud
2
qsar
2
molecule
2
pdb
2
pdb-files
2
phylogenetics
2
scanpy
2
scverse
2
transcriptomics
2
bioinformatics-pipeline
2
parameter-optimization
1
clustering
1
robustness
1
gui-framework
1
unsupervised-learning
1
blueobelisk
1
code4lib
1
java
1
conda
1
conda-environment
1
scientific
1
molecular-visualization
1
cell-design
1
cobra
1
flux
1
high-throughput-sequencing
1
crystal-structure
1
crystallography
1
indexing-algorithms
1
materials-science
1
python3
1
orange
1
orange-bioinformatics
1
metanetx-assets
1
sql
1
fracminhash
1
kmer
1
minhash
1
rust
1
scaled-minhash
1
sketching
1
sourmash
1
taxonomic-classification
1
taxonomic-profiling
1
protein
1
cluster
1
flowr
1
tsv
1
sequence-analysis
1
calculate-indices
1
peptides
1
protein-sequences
1
biojs
1
htseq
1
microarray
1
rna-seq
1
rna-sequencing
1