Packages with Software Mentions in Scientific Papers

cran: pastecs

Package for Analysis of Space-Time Ecological Series
Papers that mentioned: 44

Very Likely Science (85)

cran: pracma

Practical Numerical Math Functions
Papers that mentioned: 44

Very Likely Science (85)

pypi: wget

pure python download utility
Papers that mentioned: 43

Likely Science (55)

pypi: h2o

H2O, Fast Scalable Machine Learning, for python
Papers that mentioned: 43

Very Likely Science (100)

pypi: CFA

China Futures Assistant 中国期货助手
Papers that mentioned: 43

Very Likely Science (65)

pypi: CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data
Papers that mentioned: 43

Very Likely Science (100)

pypi: bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis
Papers that mentioned: 43

Very Likely Science (100)

cran: NLP

Natural Language Processing Infrastructure
Papers that mentioned: 43

Very Likely Science (75)

bioconductor: multiMiR

Integration of multiple microRNA-target databases with their disease and drug associations
Papers that mentioned: 43

Very Likely Science (100)

cran: AMOEBA

A Multidirectional Optimum Ecotope-Based Algorithm
Papers that mentioned: 43

Very Likely Science (85)

cran: FME

A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis
Papers that mentioned: 43

Very Likely Science (85)

cran: R2OpenBUGS

Running OpenBUGS from R
Papers that mentioned: 43

Very Likely Science (75)

pypi: Escher

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Metabolic Pathways
Papers that mentioned: 43

Very Likely Science (90)

pypi: omega

Symbolic algorithms for solving games of infinite duration.
Papers that mentioned: 43

Very Likely Science (95)

cran: partykit

A Toolkit for Recursive Partytioning
Papers that mentioned: 43

Very Likely Science (75)

cran: h2o

R Interface for the 'H2O' Scalable Machine Learning Platform
Papers that mentioned: 43

Very Likely Science (100)

cran: rgbif

Interface to the Global Biodiversity Information Facility API
Papers that mentioned: 42

Very Likely Science (75)

pypi: Integration

A simple program to perfom integration
Papers that mentioned: 42

Very Likely Science (65)

pypi: IsoCor

IsoCor: Isotope Correction for mass spectrometry labeling experiments
Papers that mentioned: 42

Very Likely Science (100)

pypi: kit

Flask, Celery, SQLAlchemy integration framework.
Papers that mentioned: 42

Very Likely Science (65)

cran: GPArotation

Gradient Projection Factor Rotation
Papers that mentioned: 42

Very Likely Science (75)

cran: rfPermute

Estimate Permutation p-Values for Random Forest Importance Metrics
Papers that mentioned: 42

Very Likely Science (85)

cran: nparcomp

Multiple Comparisons and Simultaneous Confidence Intervals
Papers that mentioned: 42

Very Likely Science (75)

cran: SCI

Standardized Climate Indices Such as SPI, SRI or SPEI
Papers that mentioned: 42

Very Likely Science (75)

pypi: lasso

A simple lasso package
Papers that mentioned: 42

Very Likely Science (65)

pypi: sm

ssh host command manager tool
Papers that mentioned: 42

Very Likely Science (65)

pypi: icoshift

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra
Papers that mentioned: 42

Very Likely Science (80)

cran: sm

Smoothing Methods for Nonparametric Regression and Density Estimation
Papers that mentioned: 42

Very Likely Science (93)

cran: DDRTree

Learning Principal Graphs with DDRTree
Papers that mentioned: 42

Very Likely Science (83)

cran: arules

Mining Association Rules and Frequent Itemsets
Papers that mentioned: 42

Very Likely Science (100)

pypi: BESST

Scaffolder for genomic assemblies.
Papers that mentioned: 42

Very Likely Science (100)

cran: generator

Generate Data Containing Fake Personally Identifiable Information
Papers that mentioned: 42

Very Likely Science (100)

pypi: express

Safely process expressions and templates based on user input.
Papers that mentioned: 42

Very Likely Science (90)

pypi: chimera

Simple Image Generation
Papers that mentioned: 42

Very Likely Science (90)

cran: adephylo

Exploratory Analyses for the Phylogenetic Comparative Method
Papers that mentioned: 42

Very Likely Science (85)

bioconductor: genefu

Computation of Gene Expression-Based Signatures in Breast Cancer
Papers that mentioned: 42

Very Likely Science (100)

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

Very Likely Science (90)

pypi: Arachne

API for Scrapy spiders
Papers that mentioned: 42

Very Likely Science (65)

cran: marmap

Import, Plot and Analyze Bathymetric and Topographic Data
Papers that mentioned: 42

Very Likely Science (75)

pypi: arules

multi-purpose association rules analysis
Papers that mentioned: 42

Very Likely Science (75)

pypi: MAnorm

A robust model for quantitative comparison of ChIP-Seq data sets
Papers that mentioned: 42

Very Likely Science (80)

cran: pca3d

Three Dimensional PCA Plots
Papers that mentioned: 42

Likely Science (50)

cran: kit

Data Manipulation Functions Implemented in C
Papers that mentioned: 42

Very Likely Science (75)

cran: LSC

Local Statistical Complexity - Automatic Pattern Discovery in Spatio-Temporal Data
Papers that mentioned: 42

Very Likely Science (85)

pypi: BooleanNet

Boolean Network Simulation Toolbox
Papers that mentioned: 41

Very Likely Science (95)

cran: IMD

Index of Multiple Deprivation Data for the UK
Papers that mentioned: 41

Very Likely Science (90)

bioconductor: GOSim

Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Papers that mentioned: 41

Very Likely Science (100)

cran: robustbase

Basic Robust Statistics
Papers that mentioned: 41

Very Likely Science (85)

pypi: Ctrax

Ctrax: The Caltech Multiple Fly Tracker
Papers that mentioned: 41

Very Likely Science (80)

cran: ggeffects

Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Papers that mentioned: 41

Very Likely Science (100)

cran: TSP

Traveling Salesperson Problem (TSP)
Papers that mentioned: 41

Very Likely Science (100)

pypi: robustbase

A Python Based Library to Calculate Estimators (Sn, Qn, MAD, IQR)
Papers that mentioned: 41

Very Likely Science (65)

bioconductor: DriverNet

Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer
Papers that mentioned: 41

Very Likely Science (100)

pypi: scikit-bio

Data structures, algorithms and educational resources for bioinformatics.
Papers that mentioned: 41

Very Likely Science (90)

cran: Canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing
Papers that mentioned: 41

Very Likely Science (100)

cran: RBF

Robust Backfitting
Papers that mentioned: 41

Very Likely Science (75)

bioconductor: apeglm

Approximate posterior estimation for GLM coefficients
Papers that mentioned: 41

Very Likely Science (98)

pypi: Solidity

Python interface for the Solidity FDEM code
Papers that mentioned: 41

Very Likely Science (65)

pypi: Haskell

Haskell-style currying in python
Papers that mentioned: 41

Very Likely Science (65)

cran: PMCMRplus

Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Papers that mentioned: 41

Very Likely Science (75)

cran: BioMark

Find Biomarkers in Two-Class Discrimination Problems
Papers that mentioned: 41

Very Likely Science (75)

pypi: parallel

Elementary parallel programming for Python
Papers that mentioned: 41

Very Likely Science (65)

pypi: Merlot

A web based project management software
Papers that mentioned: 41

Likely Science (40)

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

Very Likely Science (90)

cran: PresenceAbsence

Presence-Absence Model Evaluation
Papers that mentioned: 41

Very Likely Science (75)

pypi: eggnog-mapper

Fast functional annotation of novel sequences using eggNOG orthology assignments.
Papers that mentioned: 41

Very Likely Science (80)

pypi: lima

Lightweight Marshalling of Python 3 Objects.
Papers that mentioned: 40

Very Likely Science (65)

cran: OceanView

Visualisation of Oceanographic Data and Model Output
Papers that mentioned: 40

Very Likely Science (85)

bioconductor: PSEA

Population-Specific Expression Analysis.
Papers that mentioned: 40

Very Likely Science (85)

pypi: SIMLR

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
Papers that mentioned: 40

Very Likely Science (75)

cran: NPS

Convenience Functions and Tests for Working With the Net Promoter Score (NPS)
Papers that mentioned: 40

Very Likely Science (75)

pypi: BitBucket

Papers that mentioned: 40

Very Likely Science (65)

pypi: Hyperion

Monte-Carlo Radiative Transfer Code
Papers that mentioned: 40

Very Likely Science (65)

bioconductor: GSCA

GSCA: Gene Set Context Analysis
Papers that mentioned: 40

Very Likely Science (100)

bioconductor: OmicCircos

High-quality circular visualization of omics data
Papers that mentioned: 40

Very Likely Science (100)

cran: GSM

Gamma Shape Mixture
Papers that mentioned: 40

Very Likely Science (75)

bioconductor: SIMLR

Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Papers that mentioned: 40

Very Likely Science (65)

cran: ELT

Experience Life Tables
Papers that mentioned: 40

Very Likely Science (75)

pypi: weblogo

WebLogo3 : Sequence Logos Redrawn
Papers that mentioned: 40

Very Likely Science (70)

pypi: weka

A Python wrapper for the Weka data mining library.
Papers that mentioned: 40

Very Likely Science (90)

pypi: rpy2

Python interface to the R language (embedded R)
Papers that mentioned: 40

Very Likely Science (100)

cran: SAVER

Single-Cell RNA-Seq Gene Expression Recovery
Papers that mentioned: 40

Very Likely Science (100)

cran: r2glmm

Computes R Squared for Mixed (Multilevel) Models
Papers that mentioned: 40

Very Likely Science (85)

cran: mlogit

Multinomial Logit Models
Papers that mentioned: 40

Very Likely Science (75)

pypi: Aquarius

Aquarium IoT
Papers that mentioned: 40

Very Likely Science (80)

pypi: cox

Tools for Experiment Logging
Papers that mentioned: 40

Very Likely Science (100)

bioconductor: GeneOverlap

Test and visualize gene overlaps
Papers that mentioned: 40

Very Likely Science (95)

cran: BIOMASS

Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests
Papers that mentioned: 40

Very Likely Science (100)

bioconductor: BioNet

Routines for the functional analysis of biological networks
Papers that mentioned: 40

Very Likely Science (100)

pypi: ipython

IPython: Productive Interactive Computing
Papers that mentioned: 40

Likely Science (40)

cran: MCMCpack

Markov Chain Monte Carlo (MCMC) Package
Papers that mentioned: 40

Very Likely Science (83)

cran: Zelig

Papers that mentioned: 40

Unlikely Science (0)

pypi: EPANET

EPANET 2.0 calls from python
Papers that mentioned: 39

Very Likely Science (80)

bioconductor: KEGGgraph

KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Papers that mentioned: 39

Very Likely Science (100)

pypi: star

import star
Papers that mentioned: 39

Very Likely Science (90)

cran: glasso

Graphical Lasso: Estimation of Gaussian Graphical Models
Papers that mentioned: 39

Very Likely Science (83)

pypi: to

A trainer for PyTorch
Papers that mentioned: 39

Very Likely Science (65)

cran: runjags

Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
Papers that mentioned: 39

Very Likely Science (75)

pypi: q

Quick-and-dirty debugging output for tired programmers
Papers that mentioned: 39

Very Likely Science (65)

pypi: it

Modern python code review tool / framework
Papers that mentioned: 39

Very Likely Science (65)