Packages with Software Mentions in Scientific Papers

A pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.
Papers that mentioned: 20

Very Likely Science (100)

pypi: solver

Math problem solver
Papers that mentioned: 20

Very Likely Science (80)

cran: relsurv

Relative Survival
Papers that mentioned: 20

Very Likely Science (83)

pypi: Snowball

Investment strategy backtesting tool
Papers that mentioned: 20

Very Likely Science (65)

pypi: skyline

Papers that mentioned: 20

Unlikely Science (0)

pypi: LigParGen

Python script to provide BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.
Papers that mentioned: 20

Very Likely Science (100)

pypi: SEIR

SEIR modelling of covid19
Papers that mentioned: 20

Very Likely Science (75)

pypi: Pylon

Port of MATPOWER to Python.
Papers that mentioned: 19

Very Likely Science (100)

pypi: pytraj

Python API for cpptraj: a data analysis package for biomolecular simulation
Papers that mentioned: 19

Very Likely Science (100)

cran: Massign

Simple Matrix Construction
Papers that mentioned: 19

Very Likely Science (75)

cran: tidyLPA

Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Papers that mentioned: 19

Very Likely Science (100)

pypi: gprofiler

Python port of the R wrapper for the g:Profiler functional enrichment tool.
Papers that mentioned: 19

Very Likely Science (100)

cran: ergm

Fit, Simulate and Diagnose Exponential-Family Models for Networks
Papers that mentioned: 19

Very Likely Science (85)

pypi: mygene

Python Client for MyGene.Info services.
Papers that mentioned: 19

Very Likely Science (100)

pypi: ARGs-OAP

test version
Papers that mentioned: 19

Very Likely Science (65)

pypi: robust

Robust computational geometry predicates.
Papers that mentioned: 19

Very Likely Science (75)

cran: DrImpute

Imputing Dropout Events in Single-Cell RNA-Sequencing Data
Papers that mentioned: 19

Very Likely Science (100)

pypi: capture

Capture stdout and/or stderr
Papers that mentioned: 19

Very Likely Science (65)

bioconductor: ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Papers that mentioned: 19

Very Likely Science (100)

pypi: Meteor

Mediator pattern, interface inspired by jbogard/MediatR
Papers that mentioned: 19

Very Likely Science (65)

pypi: TextGrid

Praat TextGrid manipulation.
Papers that mentioned: 19

Very Likely Science (65)

pypi: SLC

A tool that allows you to connect to and run SQL commands to an SQLite3 database easily.
Papers that mentioned: 19

Very Likely Science (65)

cran: fBasics

Rmetrics - Markets and Basic Statistics
Papers that mentioned: 19

Very Likely Science (100)

pypi: Menu

Easily create command-line menus
Papers that mentioned: 19

Very Likely Science (65)

pypi: bias

tools to track statistical bias
Papers that mentioned: 19

Very Likely Science (90)

cran: BSDA

Basic Statistics and Data Analysis
Papers that mentioned: 19

Very Likely Science (100)

pypi: ridge

Python Machine Learning Library specialized in L2R and Recommendation.
Papers that mentioned: 19

Very Likely Science (75)

pypi: repDNA

a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects
Papers that mentioned: 19

Very Likely Science (80)

cran: ridge

Ridge Regression with Automatic Selection of the Penalty Parameter
Papers that mentioned: 19

Very Likely Science (85)

cran: MFDFA

MultiFractal Detrended Fluctuation Analysis
Papers that mentioned: 19

Very Likely Science (85)

cran: modEvA

Model Evaluation and Analysis
Papers that mentioned: 19

Very Likely Science (85)

pypi: NaiveBayes

A Naive Bayes classifier
Papers that mentioned: 19

Very Likely Science (80)

pypi: Fiona

Fiona reads and writes spatial data files
Papers that mentioned: 19

Very Likely Science (100)

bioconductor: PADOG

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Papers that mentioned: 19

Very Likely Science (100)

pypi: RTM

Numerical Computations for Radiative Transfer Modelling
Papers that mentioned: 19

Very Likely Science (75)

bioconductor: flowStats

Statistical methods for the analysis of flow cytometry data
Papers that mentioned: 19

Very Likely Science (100)

cran: MSSQL

Tools to Work with Microsoft SQL Server Databases via 'RODBC'
Papers that mentioned: 19

Very Likely Science (75)

cran: micropan

Microbial Pan-Genome Analysis
Papers that mentioned: 19

Very Likely Science (85)

pypi: Shapely

Manipulation and analysis of geometric objects
Papers that mentioned: 19

Very Likely Science (100)

pypi: xls

XLS Parsing (from js-xls)
Papers that mentioned: 19

Very Likely Science (80)

cran: grpreg

Regularization Paths for Regression Models with Grouped Covariates
Papers that mentioned: 19

Very Likely Science (100)

pypi: filter

Papers that mentioned: 19

Very Likely Science (65)

cran: survRM2

Comparing Restricted Mean Survival Time
Papers that mentioned: 19

Very Likely Science (83)

cran: doSNOW

Foreach Parallel Adaptor for the 'snow' Package
Papers that mentioned: 19

Very Likely Science (75)

pypi: GenomeBrowser

Python classes for making Genomebrowser snapshots.
Papers that mentioned: 19

Very Likely Science (80)

cran: EpiModel

Mathematical Modeling of Infectious Disease Dynamics
Papers that mentioned: 19

Very Likely Science (93)

bioconductor: MassSpecWavelet

Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Papers that mentioned: 19

Very Likely Science (100)

bioconductor: EGAD

Extending guilt by association by degree
Papers that mentioned: 19

Very Likely Science (90)

cran: ggm

Graphical Markov Models with Mixed Graphs
Papers that mentioned: 19

Very Likely Science (75)

pypi: rand

Generate String from regex pattern
Papers that mentioned: 19

Very Likely Science (65)

cran: metaplot

Data-Driven Plot Design
Papers that mentioned: 19

Very Likely Science (75)

bioconductor: mygene

Access MyGene.Info_ services
Papers that mentioned: 19

Very Likely Science (83)

cran: medflex

Flexible Mediation Analysis Using Natural Effect Models
Papers that mentioned: 19

Very Likely Science (100)

cran: cosinor

Tools for Estimating and Predicting the Cosinor Model
Papers that mentioned: 19

Very Likely Science (77)

bioconductor: GeneMeta

MetaAnalysis for High Throughput Experiments
Papers that mentioned: 19

Very Likely Science (75)

cran: DIME

Differential Identification using Mixture Ensemble
Papers that mentioned: 19

Very Likely Science (93)

cran: pomp

Statistical Inference for Partially Observed Markov Processes
Papers that mentioned: 19

Very Likely Science (100)

pypi: SC

Easily control SuperCollider sound server from python
Papers that mentioned: 19

Very Likely Science (65)

cran: SGP

Student Growth Percentiles & Percentile Growth Trajectories
Papers that mentioned: 19

Very Likely Science (75)

bioconductor: Cardinal

A mass spectrometry imaging toolbox for statistical analysis
Papers that mentioned: 19

Very Likely Science (100)

cran: Deducer

A Data Analysis GUI for R
Papers that mentioned: 19

Very Likely Science (85)

bioconductor: RPA

RPA: Robust Probabilistic Averaging for probe-level analysis
Papers that mentioned: 19

Very Likely Science (100)

bioconductor: PAA

PAA (Protein Array Analyzer)
Papers that mentioned: 19

Very Likely Science (90)

pypi: Collector

Visym Collector
Papers that mentioned: 19

Very Likely Science (100)

pypi: designer

Student-friendly and evidence-based visual graphics library.
Papers that mentioned: 19

Very Likely Science (100)

pypi: DAWG

Fast and memory efficient DAWG (DAFSA) for Python
Papers that mentioned: 19

Very Likely Science (95)

cran: POINT

Protein Structure Guided Local Test
Papers that mentioned: 19

Very Likely Science (75)

pypi: instrument

instrumentation primitives for metrics and benchmarking
Papers that mentioned: 19

Very Likely Science (65)

pypi: MUSiCC

MUSICC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome.
Papers that mentioned: 19

Likely Science (40)

pypi: lab

Benchmark your code
Papers that mentioned: 19

Very Likely Science (100)

pypi: OpenElectrophy

OpenElectrophy : an electrophysiological data- and analysis-sharing framework
Papers that mentioned: 19

Very Likely Science (90)

cran: SLC

Slope and level change
Papers that mentioned: 19

Very Likely Science (75)

pypi: VGA

Python package implements the Group Additivity (GA) method for estimating thermodynamic properties
Papers that mentioned: 19

Very Likely Science (100)

pypi: pomp

Screen scraping and web crawling framework
Papers that mentioned: 19

Very Likely Science (65)

cran: biclust

BiCluster Algorithms
Papers that mentioned: 19

Very Likely Science (85)

pypi: mapview

A kivy garden mapview demo.
Papers that mentioned: 19

Very Likely Science (65)

pypi: scLVM

scLVM
Papers that mentioned: 19

Very Likely Science (100)

cran: mapview

Interactive Viewing of Spatial Data in R
Papers that mentioned: 19

Very Likely Science (79)

pypi: pydicom

A pure Python package for reading and writing DICOM data
Papers that mentioned: 19

Very Likely Science (80)

pypi: IES

iPIPA
Papers that mentioned: 19

Very Likely Science (80)

pypi: DASP

a library for DS CAA Developer
Papers that mentioned: 19

Very Likely Science (65)

cran: zTree

Functions to Import Data from 'z-Tree' into R
Papers that mentioned: 19

Very Likely Science (75)

pypi: chart

chart
Papers that mentioned: 19

Very Likely Science (80)

cran: pathfindR

Enrichment Analysis Utilizing Active Subnetworks
Papers that mentioned: 19

Very Likely Science (95)

pypi: metaplot

metaplot
Papers that mentioned: 19

Very Likely Science (65)

pypi: MFDFA

Multifractal Detrended Fluctuation Analysis in Python
Papers that mentioned: 19

Very Likely Science (100)

pypi: S4

Fast and cheap synchronisation of files using Amazon S3
Papers that mentioned: 19

Unlikely Science (15)

pypi: beta

Develop soon
Papers that mentioned: 19

Very Likely Science (65)

pypi: clustalo

Python wrapper around libclustalo
Papers that mentioned: 19

Very Likely Science (65)

cran: robust

Port of the S+ "Robust Library"
Papers that mentioned: 19

Very Likely Science (75)

cran: EFS

Tool for Ensemble Feature Selection
Papers that mentioned: 19

Very Likely Science (75)

cran: BacArena

Modeling Framework for Cellular Communities in their Environments
Papers that mentioned: 19

Very Likely Science (93)

pypi: theta

Deep learning toolbox for end-to-end text information extraction tasks.
Papers that mentioned: 19

Very Likely Science (90)

pypi: Calculations

To calculate equations and draw diagrams
Papers that mentioned: 18

Very Likely Science (80)