Packages with Software Mentions in Scientific Papers

pypi: Risk

Objects and mthods for playing the boardgame Risk
Papers that mentioned: 114

pypi: Sift

Python bindings for Sift Science's API
Papers that mentioned: 114

pypi: biopython

Freely available tools for computational molecular biology.
Papers that mentioned: 114

cran: Recon

Computational Tools for Economics
Papers that mentioned: 114

cran: bbmle

Tools for General Maximum Likelihood Estimation
Papers that mentioned: 114

bioconductor: microbiome

Microbiome Analytics
Papers that mentioned: 114

cran: Risk

Computes 26 Financial Risk Measures for Any Continuous Distribution
Papers that mentioned: 114

cran: bnlearn

Bayesian Network Structure Learning, Parameter Learning and Inference
Papers that mentioned: 113

cran: gamlss

Generalised Additive Models for Location Scale and Shape
Papers that mentioned: 113

pypi: bnlearn

Python package for learning the graphical structure of Bayesian networks, parameter learning, inference and sampling methods.
Papers that mentioned: 113

bioconductor: scran

Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113

cran: biomod2

Ensemble Platform for Species Distribution Modeling
Papers that mentioned: 113

cran: DOT

Render and Export DOT Graphs in R
Papers that mentioned: 112

cran: gam

Generalized Additive Models
Papers that mentioned: 112

cran: mvmeta

Multivariate and Univariate Meta-Analysis and Meta-Regression
Papers that mentioned: 112

cran: ExomeDepth

Calls Copy Number Variants from Targeted Sequence Data
Papers that mentioned: 112

cran: mvabund

Statistical Methods for Analysing Multivariate Abundance Data
Papers that mentioned: 112

pypi: gam

Global Explanations for Deep Neural Networks
Papers that mentioned: 112

cran: geosphere

Spherical Trigonometry
Papers that mentioned: 112

bioconductor: PROMISE

PRojection Onto the Most Interesting Statistical Evidence
Papers that mentioned: 111

cran: gamm4

Generalized Additive Mixed Models using 'mgcv' and 'lme4'
Papers that mentioned: 111

cran: GAD

Analysis of variance from general principles
Papers that mentioned: 111

cran: betapart

Partitioning Beta Diversity into Turnover and Nestedness Components
Papers that mentioned: 111

cran: fmsb

Functions for Medical Statistics Book with some Demographic Data
Papers that mentioned: 111

pypi: sas

Python split annotations library
Papers that mentioned: 111

pypi: khmer

khmer k-mer counting library
Papers that mentioned: 110

cran: seqinr

Biological Sequences Retrieval and Analysis
Papers that mentioned: 110

cran: SIBER

Stable Isotope Bayesian Ellipses in R
Papers that mentioned: 110

pypi: Chroma

Color handling made simple.
Papers that mentioned: 110

pypi: networkx

Python package for creating and manipulating graphs and networks
Papers that mentioned: 110

cran: plotrix

Various Plotting Functions
Papers that mentioned: 110

pypi: Trump

Persistent Objectified Indexed Data
Papers that mentioned: 109

cran: smatr

(Standardised) Major Axis Estimation and Testing Routines
Papers that mentioned: 109

bioconductor: flowCore

flowCore: Basic structures for flow cytometry data
Papers that mentioned: 109

pypi: Watson

The Chatbot that won America's hearts in the 80's is back! And this time, he means business!
Papers that mentioned: 108

pypi: gmx

GROMACS Python module
Papers that mentioned: 108

pypi: db

Databases for Humans
Papers that mentioned: 108

cran: mstate

Data Preparation, Estimation and Prediction in Multi-State Models
Papers that mentioned: 108

cran: NMF

Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
Papers that mentioned: 108

pypi: Distance

Utilities for comparing sequences
Papers that mentioned: 108

cran: Distance

Distance Sampling Detection Function and Abundance Estimation
Papers that mentioned: 108

cran: EMT

Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data
Papers that mentioned: 108

bioconductor: wateRmelon

Illumina 450 and EPIC methylation array normalization and metrics
Papers that mentioned: 108

cran: magrittr

A Forward-Pipe Operator for R
Papers that mentioned: 107

cran: origin

Explicitly Qualifying Namespaces by Automatically Adding 'pkg::' to Functions
Papers that mentioned: 107

pypi: origin

Python library for the Origin Event Publisher
Papers that mentioned: 107

bioconductor: rtracklayer

R interface to genome annotation files and the UCSC genome browser
Papers that mentioned: 107

pypi: SIR

SDN Internet Router
Papers that mentioned: 107

cran: Amelia

A Program for Missing Data
Papers that mentioned: 106

cran: AF

Model-Based Estimation of Confounder-Adjusted Attributable Fractions
Papers that mentioned: 106

pypi: GN

a hierachical community detection algorithm by Girvan Newman
Papers that mentioned: 106

cran: betareg

Beta Regression
Papers that mentioned: 106

cran: ez

Easy Analysis and Visualization of Factorial Experiments
Papers that mentioned: 106

pypi: phred

Phred text editor
Papers that mentioned: 105

cran: epitools

Epidemiology Tools
Papers that mentioned: 105

pypi: node2vec

Implementation of the node2vec algorithm
Papers that mentioned: 104

pypi: scales

Stats for Python processes
Papers that mentioned: 104

cran: node2vec

Algorithmic Framework for Representational Learning on Graphs
Papers that mentioned: 104

bioconductor: Biobase

Biobase: Base functions for Bioconductor
Papers that mentioned: 104

cran: scales

Scale Functions for Visualization
Papers that mentioned: 104

pypi: figshare

Command-line client for figshare API
Papers that mentioned: 103

pypi: Health

Healthcare research tools
Papers that mentioned: 103

pypi: i

Never use print() to debug again; inspect variables, expressions, and program execution with a single, simple function call.
Papers that mentioned: 103

cran: geoR

Analysis of Geostatistical Data
Papers that mentioned: 102

pypi: AltAnalyze

User Friendly Application for Comprehensive Transcriptome Analysis
Papers that mentioned: 102

pypi: SVR

Used to retrieve the latest version of a software and will return it as a string
Papers that mentioned: 102

pypi: nls

NLS: Non-Linear Schrodinger equation solver.
Papers that mentioned: 102

cran: EMD

Empirical Mode Decomposition and Hilbert Spectral Analysis
Papers that mentioned: 102

pypi: pythia

An extensible, object-oriented framework for specifying and staging complex, multi-physics simulations.
Papers that mentioned: 102

cran: pbkrtest

Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
Papers that mentioned: 102

pypi: CAGE

A generic and fairly complete cellular automata simulation engine.
Papers that mentioned: 101

pypi: figtree

Multi-format configuration assembler
Papers that mentioned: 100

cran: DSSAT

A Comprehensive R Interface for the DSSAT Cropping Systems Model
Papers that mentioned: 100

cran: mixtools

Tools for Analyzing Finite Mixture Models
Papers that mentioned: 100

cran: effsize

Efficient Effect Size Computation
Papers that mentioned: 100

Circuitscape borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes.
Papers that mentioned: 100