Packages with Software Mentions in Scientific Papers

Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size
Papers that mentioned: 11

Very Likely Science (75)

cran: energy

E-Statistics: Multivariate Inference via the Energy of Data
Papers that mentioned: 11

Very Likely Science (100)

bioconductor: OrderedList

Similarities of Ordered Gene Lists
Papers that mentioned: 11

Very Likely Science (98)

cran: janitor

Simple Tools for Examining and Cleaning Dirty Data
Papers that mentioned: 11

Very Likely Science (100)

pypi: copycat

copycat - simple, transparent and non-intrusive python persistence
Papers that mentioned: 11

Very Likely Science (65)

pypi: f

Functional tools, collections and monads.
Papers that mentioned: 11

Very Likely Science (65)

pypi: spectrometer

UNKNOWN
Papers that mentioned: 11

Very Likely Science (65)

pypi: guanaco

3D CTF correction
Papers that mentioned: 11

Very Likely Science (100)

cran: PCAmixdata

Multivariate Analysis of Mixed Data
Papers that mentioned: 11

Very Likely Science (85)

pypi: SpikeSort

Python Spike Sorting Package
Papers that mentioned: 11

Very Likely Science (80)

pypi: de

de
Papers that mentioned: 11

Very Likely Science (65)

pypi: here

Configures shells for easy python development
Papers that mentioned: 11

Very Likely Science (65)

pypi: MultiMap

Mapping class which allows multiple values per key and preserves order by value; values with the same key are not grouped together.
Papers that mentioned: 11

Very Likely Science (65)

cran: SHIP

SHrinkage covariance Incorporating Prior knowledge
Papers that mentioned: 11

Very Likely Science (60)

pypi: corr

Interfaces to CASPER correlators
Papers that mentioned: 11

Very Likely Science (80)

cran: smoothHR

Smooth Hazard Ratio Curves Taking a Reference Value
Papers that mentioned: 11

Very Likely Science (80)

bioconductor: methylGSA

Gene Set Analysis Using the Outcome of Differential Methylation
Papers that mentioned: 11

Very Likely Science (100)

pypi: season

season wiz web framework
Papers that mentioned: 11

Very Likely Science (85)

pypi: hcluster

A hierarchical clustering package for Scipy.
Papers that mentioned: 11

Very Likely Science (80)

cran: tmle

Targeted Maximum Likelihood Estimation
Papers that mentioned: 11

Very Likely Science (83)

pypi: biom-format

Biological Observation Matrix (BIOM) format
Papers that mentioned: 11

Very Likely Science (80)

cran: RAMClustR

Mass Spectrometry Metabolomics Feature Clustering and Interpretation
Papers that mentioned: 11

Very Likely Science (100)

cran: RMediation

Mediation Analysis Confidence Intervals
Papers that mentioned: 11

Very Likely Science (85)

pypi: seqlogo

Python port of the R Bioconductor `seqlogo` package
Papers that mentioned: 11

Very Likely Science (75)

cran: PoA

Finds the Price of Anarchy for Routing Games
Papers that mentioned: 11

Likely Science (58)

pypi: hclust2

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication
Papers that mentioned: 11

Very Likely Science (100)

cran: biomartr

Genomic Data Retrieval
Papers that mentioned: 11

Very Likely Science (100)

pypi: Edward

A library for probabilistic modeling, inference, and criticism
Papers that mentioned: 11

Very Likely Science (90)

cran: Rphylopars

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Papers that mentioned: 11

Very Likely Science (100)

pypi: dms_tools

Deep mutational scanning (DMS) analysis tools.
Papers that mentioned: 11

Very Likely Science (100)

pypi: glide

Easy ETL
Papers that mentioned: 11

Very Likely Science (65)

pypi: bank

Core Banking for Python
Papers that mentioned: 11

Very Likely Science (65)

pypi: clustergram

Clustergram - visualization and diagnostics for cluster analysis
Papers that mentioned: 11

Very Likely Science (100)

pypi: eig

Enhanced Integrated Gradients - a method of attributing the prediction of a deep network to its input features
Papers that mentioned: 11

Likely Science (50)

pypi: value

Implementation of Value Object pattern
Papers that mentioned: 11

Very Likely Science (65)

cran: permute

Functions for Generating Restricted Permutations of Data
Papers that mentioned: 11

Very Likely Science (75)

pypi: glibc

Pure-Python bindings to glibc (based on ctypes)
Papers that mentioned: 11

Very Likely Science (65)

cran: Cairo

R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output
Papers that mentioned: 11

Very Likely Science (85)

pypi: egg

This is a lonely egg.
Papers that mentioned: 11

Very Likely Science (65)

cran: censReg

Censored Regression (Tobit) Models
Papers that mentioned: 11

Very Likely Science (85)

pypi: mira

A package for simplifying object detection
Papers that mentioned: 11

Very Likely Science (65)

cran: assignPOP

Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework
Papers that mentioned: 11

Very Likely Science (100)

pypi: p4

A Python Pre-Processor for the Processing system
Papers that mentioned: 11

Very Likely Science (80)

cran: arulesViz

Visualizing Association Rules and Frequent Itemsets
Papers that mentioned: 11

Very Likely Science (100)

pypi: classifier

Classify the files in your Downloads folder into suitable destinations.
Papers that mentioned: 11

Very Likely Science (85)

cran: AGHmatrix

Relationship Matrices for Diploid and Autopolyploid Species
Papers that mentioned: 11

Very Likely Science (100)

cran: RecordLinkage

Record Linkage Functions for Linking and Deduplicating Data Sets
Papers that mentioned: 11

Very Likely Science (75)

cran: influence.ME

Tools for Detecting Influential Data in Mixed Effects Models
Papers that mentioned: 11

Very Likely Science (85)

cran: TRES

Tensor Regression with Envelope Structure
Papers that mentioned: 11

Very Likely Science (100)

bioconductor: TDARACNE

Papers that mentioned: 11

Unlikely Science (0)

pypi: CAI

Python implementation of codon adaptation index
Papers that mentioned: 11

Very Likely Science (100)

bioconductor: flowPeaks

An R package for flow data clustering
Papers that mentioned: 11

Very Likely Science (75)

cran: inbreedR

Analysing Inbreeding Based on Genetic Markers
Papers that mentioned: 11

Very Likely Science (85)

bioconductor: AnnotationForge

Tools for building SQLite-based annotation data packages
Papers that mentioned: 11

Very Likely Science (75)

cran: hash

Full Featured Implementation of Hash Tables/Associative Arrays/Dictionaries
Papers that mentioned: 11

Very Likely Science (75)

bioconductor: methylSig

MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Papers that mentioned: 11

Very Likely Science (100)

pypi: energy

Energy system for social games
Papers that mentioned: 11

Likely Science (40)

bioconductor: Linnorm

Linear model and normality based normalization and transformation method (Linnorm)
Papers that mentioned: 11

Very Likely Science (98)

cran: RESS

Integrates R and Essentia
Papers that mentioned: 11

Very Likely Science (75)

pypi: approach

Papers that mentioned: 11

Very Likely Science (65)

bioconductor: COHCAP

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Papers that mentioned: 11

Very Likely Science (100)

pypi: log

Papers that mentioned: 11

Unlikely Science (0)

cran: moonBook

Functions and Datasets for the Book by Keon-Woong Moon
Papers that mentioned: 11

Very Likely Science (95)

cran: carData

Companion to Applied Regression Data Sets
Papers that mentioned: 11

Very Likely Science (85)

cran: EHR

Electronic Health Record (EHR) Data Processing and Analysis Tool
Papers that mentioned: 11

Very Likely Science (68)

bioconductor: makecdfenv

CDF Environment Maker
Papers that mentioned: 11

Very Likely Science (83)

pypi: Firebird

The Firebird Python library provides a pythonic interface to the Firebird API.
Papers that mentioned: 11

Very Likely Science (65)

pypi: arsenal

Papers that mentioned: 11

Unlikely Science (0)

cran: MNP

Fitting the Multinomial Probit Model
Papers that mentioned: 11

Very Likely Science (100)

cran: mitml

Tools for Multiple Imputation in Multilevel Modeling
Papers that mentioned: 11

Very Likely Science (85)

cran: IMEC

Ising Model of Explanatory Coherence
Papers that mentioned: 11

Very Likely Science (75)

cran: MLmetrics

Machine Learning Evaluation Metrics
Papers that mentioned: 11

Very Likely Science (85)

pypi: Accord

A high-level Python Web framework that encourages rapid development and clean, pragmatic design.
Papers that mentioned: 11

Likely Science (40)

cran: mdatools

Multivariate Data Analysis for Chemometrics
Papers that mentioned: 11

Very Likely Science (100)

cran: mrgsolve

Simulate from ODE-Based Models
Papers that mentioned: 11

Very Likely Science (100)

cran: Haplin

Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Papers that mentioned: 11

Very Likely Science (75)

cran: MVB

Mutivariate Bernoulli log-linear model
Papers that mentioned: 10

Very Likely Science (75)

pypi: pacman

Initially, a tool for introspecting and analysing sys.path
Papers that mentioned: 10

Very Likely Science (65)

pypi: andi

Library for annotation-based dependency injection
Papers that mentioned: 10

Very Likely Science (80)

cran: catR

Generation of IRT Response Patterns under Computerized Adaptive Testing
Papers that mentioned: 10

Very Likely Science (75)

cran: morpheus

Estimate Parameters of Mixtures of Logistic Regressions
Papers that mentioned: 10

Very Likely Science (85)

cran: InterVA4

Replicate and Analyse 'InterVA4'
Papers that mentioned: 10

Very Likely Science (75)

cran: denovolyzeR

Statistical Analyses of De Novo Genetic Variants
Papers that mentioned: 10

Very Likely Science (93)

pypi: bam

Text snippets on the command line.
Papers that mentioned: 10

Very Likely Science (65)

cran: chron

Chronological Objects which Can Handle Dates and Times
Papers that mentioned: 10

Likely Science (50)

pypi: SVC

Spreadsheet Viewer and Converter
Papers that mentioned: 10

Very Likely Science (65)

cran: digest

Create Compact Hash Digests of R Objects
Papers that mentioned: 10

Very Likely Science (100)

pypi: amira

Automated Malware Incident Response and Analysis
Papers that mentioned: 10

Very Likely Science (75)

cran: HaploSim

Functions to Simulate Haplotypes
Papers that mentioned: 10

Very Likely Science (75)

pypi: fc

Enables Python to be functionally chain-styled.
Papers that mentioned: 10

Very Likely Science (65)

cran: edgeRun

More Powerful Unconditional Testing of Negative Binomial Means for Digital Gene Expression Data
Papers that mentioned: 10

Very Likely Science (85)