Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
pypi projects 9,932
pypi: Mallet
Mallet is a tool for building and maintaining Debian-based virtual servers for web application hosting.Papers that mentioned: 46
pypi: snakemake
Workflow management system to create reproducible and scalable data analysesPapers that mentioned: 45
pypi: gee
gee (good enough encryption): the simplest possible encryption tool for single files.Papers that mentioned: 45
pypi: DANE
Utils for working with the Distributed Annotation and Enrichment systemPapers that mentioned: 44
pypi: com
Papers that mentioned: 44pypi: CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing dataPapers that mentioned: 43
pypi: bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysisPapers that mentioned: 43
pypi: Escher
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic PathwaysPapers that mentioned: 43
pypi: IsoCor
IsoCor: Isotope Correction for mass spectrometry labeling experimentsPapers that mentioned: 42
pypi: MAnorm
A robust model for quantitative comparison of ChIP-Seq data setsPapers that mentioned: 42
pypi: MinimPy
MinimPy is a desktop application program for sequential allocation of subjects to treatment groups in clinical trials by using the method of minimisation.Papers that mentioned: 42
pypi: express
Safely process expressions and templates based on user input.Papers that mentioned: 42
pypi: icoshift
icoshift: A versatile tool for the rapid alignment of 1D NMR spectraPapers that mentioned: 42
pypi: eggnog-mapper
Fast functional annotation of novel sequences using eggNOG orthology assignments.Papers that mentioned: 41
pypi: pdb2pqr
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.Papers that mentioned: 41
pypi: robustbase
A Python Based Library to Calculate Estimators (Sn, Qn, MAD, IQR)Papers that mentioned: 41
pypi: scikit-bio
Data structures, algorithms and educational resources for bioinformatics.Papers that mentioned: 41
pypi: SIMLR
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learningPapers that mentioned: 40
pypi: BitBucket
Papers that mentioned: 40pypi: GenDoc
Generate a Markdown Documentation file from a Python Repository with DocStrings.Papers that mentioned: 39
pypi: lifelines
Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regressionPapers that mentioned: 39
pypi: jupyter
Jupyter metapackage. Install all the Jupyter components in one go.Papers that mentioned: 39
pypi: Rest
Rest is a rest client for python that makes it easy to make authenticated rest calls.Papers that mentioned: 39
pypi: LDpred
A Python package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD)Papers that mentioned: 38
pypi: Poly
rapid development of embarrassingly parallelizable applicationsPapers that mentioned: 38
pypi: imbalanced-learn
Toolbox for imbalanced dataset in machine learning.Papers that mentioned: 38
pypi: multiqc
Create aggregate bioinformatics analysis reports across many samples and toolsPapers that mentioned: 37
pypi: Dovetail
A light-weight, multi-platform, build tool for Python with Continuous Integration servers like Jenkins in mind.Papers that mentioned: 37