Packages with Software Mentions in Scientific Papers

bioconductor: DEsingle

DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Papers that mentioned: 15

Very Likely Science (100)

pypi: connectivity

Library containing Server and Client for transferring messages and files via TCP
Papers that mentioned: 15

Very Likely Science (65)

cran: olsrr

Tools for Building OLS Regression Models
Papers that mentioned: 15

Very Likely Science (100)

pypi: deblur

Deblur
Papers that mentioned: 15

Very Likely Science (100)

pypi: algebra

Algebraic structures
Papers that mentioned: 15

Very Likely Science (65)

pypi: Elixir

Declarative Mapper for SQLAlchemy
Papers that mentioned: 15

Very Likely Science (65)

pypi: scythe

Find best matching set of transcripts for one-to-one orthologous genes from two or more species
Papers that mentioned: 15

Very Likely Science (80)

cran: metap

Meta-Analysis of Significance Values
Papers that mentioned: 15

Very Likely Science (85)

pypi: nibabel

Access a multitude of neuroimaging data formats
Papers that mentioned: 15

Very Likely Science (80)

cran: NST

Normalized Stochasticity Ratio
Papers that mentioned: 15

Very Likely Science (100)

bioconductor: annotatr

Annotation of Genomic Regions to Genomic Annotations
Papers that mentioned: 15

Very Likely Science (100)

bioconductor: VariantTools

Tools for Exploratory Analysis of Variant Calls
Papers that mentioned: 15

Very Likely Science (100)

cran: gkmSVM

Gapped-Kmer Support Vector Machine
Papers that mentioned: 15

Very Likely Science (83)

cran: LinkageMapView

Plot Linkage Group Maps with Quantitative Trait Loci
Papers that mentioned: 15

Very Likely Science (100)

bioconductor: sigPathway

Pathway Analysis
Papers that mentioned: 15

Very Likely Science (100)

pypi: mcr

Papers that mentioned: 15

Very Likely Science (65)

bioconductor: CSAR

Statistical tools for the analysis of ChIP-seq data
Papers that mentioned: 15

Very Likely Science (100)

bioconductor: PROcess

Ciphergen SELDI-TOF Processing
Papers that mentioned: 15

Very Likely Science (98)

cran: LOGICOIL

multi-state prediction of coiled-coil oligomeric state
Papers that mentioned: 15

Very Likely Science (75)

pypi: pyLDAvis

Interactive topic model visualization. Port of the R package.
Papers that mentioned: 15

Very Likely Science (100)

cran: C50

C5.0 Decision Trees and Rule-Based Models
Papers that mentioned: 15

Very Likely Science (99)

cran: brglm2

Bias Reduction in Generalized Linear Models
Papers that mentioned: 15

Very Likely Science (100)

cran: metaMA

Meta-Analysis for MicroArrays
Papers that mentioned: 15

Very Likely Science (85)

cran: rotl

Interface to the 'Open Tree of Life' API
Papers that mentioned: 15

Very Likely Science (100)

bioconductor: RCM

Fit row-column association models with the negative binomial distribution for the microbiome
Papers that mentioned: 15

Very Likely Science (90)

pypi: ALM

ALM Model in Python
Papers that mentioned: 15

Very Likely Science (65)

cran: lda

Collapsed Gibbs Sampling Methods for Topic Models
Papers that mentioned: 15

Very Likely Science (75)

pypi: pop

The Plugin Oriented Programming System
Papers that mentioned: 15

Very Likely Science (65)

pypi: Pyomo

Pyomo: Python Optimization Modeling Objects
Papers that mentioned: 15

Very Likely Science (100)

pypi: nstruct

Define complicate C/C++ structs in Python to parse/pack them from/to raw bytes
Papers that mentioned: 15

Very Likely Science (65)

pypi: skygrid

The SkyGrid Python SDK
Papers that mentioned: 15

Very Likely Science (65)

pypi: piano

CMS built using Pyramid and MongoDB
Papers that mentioned: 15

Likely Science (40)

pypi: pantomime

MIME type normalisation and labels.
Papers that mentioned: 15

Very Likely Science (80)

pypi: genesis

Implementation of FreeSWITCH Event Socket protocol with asyncio
Papers that mentioned: 15

Very Likely Science (65)

cran: Relatedness

Maximum Likelihood Estimation of Relatedness using EM Algorithm
Papers that mentioned: 15

Very Likely Science (85)

cran: networktools

Tools for Identifying Important Nodes in Networks
Papers that mentioned: 15

Very Likely Science (85)

cran: EEM

Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data
Papers that mentioned: 15

Very Likely Science (81)

bioconductor: flowDensity

Sequential Flow Cytometry Data Gating
Papers that mentioned: 15

Very Likely Science (90)

pypi: free

Free yourself from CAPTCHAs!
Papers that mentioned: 15

Very Likely Science (80)

pypi: IGC

Papers that mentioned: 15

Very Likely Science (65)

pypi: Therapy

Toy blog software using Haus on CouchDB.
Papers that mentioned: 15

Likely Science (40)

cran: free

Flexible Regularized Estimating Equations
Papers that mentioned: 15

Very Likely Science (75)

pypi: Runner

Simple command runner
Papers that mentioned: 15

Very Likely Science (65)

pypi: SloppyCell

Papers that mentioned: 15

Very Likely Science (80)

cran: pop

A Flexible Syntax for Population Dynamic Modelling
Papers that mentioned: 15

Very Likely Science (90)

pypi: 16

Papers that mentioned: 15

Very Likely Science (65)

cran: quanteda

Quantitative Analysis of Textual Data
Papers that mentioned: 15

Very Likely Science (93)

bioconductor: flowWorkspace

Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Papers that mentioned: 15

Very Likely Science (75)

pypi: VASA

Spatial Structure Visualization
Papers that mentioned: 15

Very Likely Science (75)

pypi: svm

Version manager for Apache Spark
Papers that mentioned: 15

Very Likely Science (65)

pypi: propka

Heuristic pKa calculations with ligands
Papers that mentioned: 15

Very Likely Science (80)

pypi: purr

Data reduction logging tool, Useful for remembering reductions
Papers that mentioned: 15

Very Likely Science (100)

pypi: quantity

Unit-safe computations with quantities (including money)
Papers that mentioned: 15

Very Likely Science (65)

pypi: What

A helper for testing process output
Papers that mentioned: 15

Very Likely Science (65)

pypi: ATS

安卓手机自动化测试驱动包.
Papers that mentioned: 15

Very Likely Science (65)

cran: Ridit

Ridit Analysis (An extension of the Kruskal-Wallis Test.)
Papers that mentioned: 15

Very Likely Science (85)

pypi: Mantis

A Minimalist ORM for Python
Papers that mentioned: 15

Very Likely Science (65)

cran: mvoutlier

Multivariate Outlier Detection Based on Robust Methods
Papers that mentioned: 15

Very Likely Science (93)

cran: optparse

Command Line Option Parser
Papers that mentioned: 15

Very Likely Science (100)

pypi: a

Python Distribution Utilities
Papers that mentioned: 15

Very Likely Science (65)

pypi: medaka

Neural network sequence error correction.
Papers that mentioned: 15

Very Likely Science (95)

bioconductor: piano

Platform for integrative analysis of omics data
Papers that mentioned: 15

Very Likely Science (100)

pypi: regress

Python bindings to Rust's regress ECMA regular expressions library
Papers that mentioned: 15

Very Likely Science (100)

pypi: GEMA

A library to build and study Self-Organizing-Maps
Papers that mentioned: 15

Very Likely Science (65)

cran: STI

Calculation of the Standardized Temperature Index
Papers that mentioned: 15

Very Likely Science (75)

pypi: MetaLab

MetaLab
Papers that mentioned: 15

Very Likely Science (65)

cran: imager

Image Processing Library Based on 'CImg'
Papers that mentioned: 15

Very Likely Science (100)

pypi: PyWavelets

PyWavelets, wavelet transform module
Papers that mentioned: 15

Very Likely Science (100)

cran: nls2

Non-Linear Regression with Brute Force
Papers that mentioned: 15

Very Likely Science (85)

bioconductor: SCnorm

Normalization of single cell RNA-seq data
Papers that mentioned: 15

Very Likely Science (100)

pypi: modeler

Reconstruct 3D models of objects from multiple images
Papers that mentioned: 15

Very Likely Science (71)

cran: blandr

Bland-Altman Method Comparison
Papers that mentioned: 15

Very Likely Science (100)

cran: COSINE

COndition SpecIfic sub-NEtwork
Papers that mentioned: 15

Very Likely Science (85)

cran: drgee

Doubly Robust Generalized Estimating Equations
Papers that mentioned: 15

Very Likely Science (75)

cran: CGP

Composite Gaussian Process Models
Papers that mentioned: 15

Very Likely Science (75)

bioconductor: ChIPQC

Quality metrics for ChIPseq data
Papers that mentioned: 15

Very Likely Science (90)

cran: LiblineaR

Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Papers that mentioned: 15

Very Likely Science (75)

cran: GDINA

The Generalized DINA Model Framework
Papers that mentioned: 15

Very Likely Science (100)

pypi: scape

a framework for raspberry pi developing
Papers that mentioned: 15

Very Likely Science (65)

bioconductor: BiocGenerics

S4 generic functions used in Bioconductor
Papers that mentioned: 15

Very Likely Science (75)

cran: ACDC

Analysis of Congruent Diversification Classes
Papers that mentioned: 15

Very Likely Science (100)

pypi: move

Moves revision-controlled files interactively in an editor.
Papers that mentioned: 15

Very Likely Science (65)

cran: box

Write Reusable, Composable and Modular R Code
Papers that mentioned: 15

Very Likely Science (77)

cran: Quartet

Comparison of Phylogenetic Trees Using Quartet and Split Measures
Papers that mentioned: 15

Very Likely Science (100)

pypi: mumin

Seamlessly build the MuMiN dataset.
Papers that mentioned: 15

Very Likely Science (96)

pypi: lda

Topic modeling with latent Dirichlet allocation
Papers that mentioned: 15

Very Likely Science (90)

cran: rEDM

Empirical Dynamic Modeling ('EDM')
Papers that mentioned: 15

Very Likely Science (85)

pypi: networktools

NetworkTools are some special functions to help with software developing
Papers that mentioned: 15

Very Likely Science (75)

pypi: HierCC

Hierarchical Clustering of cgMLST profiles
Papers that mentioned: 15

Very Likely Science (100)

cran: QuACN

Quantitative Analysis of Complex Networks
Papers that mentioned: 15

Very Likely Science (85)

cran: psycho

Efficient and Publishing-Oriented Workflow for Psychological Science
Papers that mentioned: 15

Very Likely Science (100)

pypi: PLEASE

Software for the analysis of Low Energy Electron Microscopy data
Papers that mentioned: 15

Very Likely Science (90)

cran: scape

Statistical Catch-at-Age Plotting Environment
Papers that mentioned: 15

Very Likely Science (85)

cran: regress

Gaussian Linear Models with Linear Covariance Structure
Papers that mentioned: 15

Very Likely Science (93)

cran: R2BayesX

Estimate Structured Additive Regression Models with 'BayesX'
Papers that mentioned: 15

Very Likely Science (93)

cran: shinyjs

Easily Improve the User Experience of Your Shiny Apps in Seconds
Papers that mentioned: 15

Very Likely Science (75)

cran: reldist

Relative Distribution Methods
Papers that mentioned: 15

Very Likely Science (83)

pypi: box

Papers that mentioned: 15

Unlikely Science (0)

cran: GISTools

Some further GIS capabilities for R
Papers that mentioned: 15

Very Likely Science (75)

cran: apTreeshape

Analyses of Phylogenetic Treeshape
Papers that mentioned: 15

Very Likely Science (85)